The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
A meshwork-like substance found within the extracellular space and in association with the basement membrane of the cell surface. It promotes cellular proliferation and provides a supporting structure to which cells or cell lysates in culture dishes adhere.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Macromolecular organic compounds that contain carbon, hydrogen, oxygen, nitrogen, and usually, sulfur. These macromolecules (proteins) form an intricate meshwork in which cells are embedded to construct tissues. Variations in the relative types of macromolecules and their organization determine the type of extracellular matrix, each adapted to the functional requirements of the tissue. The two main classes of macromolecules that form the extracellular matrix are: glycosaminoglycans, usually linked to proteins (proteoglycans), and fibrous proteins (e.g., COLLAGEN; ELASTIN; FIBRONECTINS; and LAMININ).
A secreted endopeptidase homologous with INTERSTITIAL COLLAGENASE, but which possesses an additional fibronectin-like domain.
A family of zinc-dependent metalloendopeptidases that is involved in the degradation of EXTRACELLULAR MATRIX components.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
The residual framework structure of the CELL NUCLEUS that maintains many of the overall architectural features of the cell nucleus including the nuclear lamina with NUCLEAR PORE complex structures, residual CELL NUCLEOLI and an extensive fibrogranular structure in the nuclear interior. (Advan. Enzyme Regul. 2002; 42:39-52)
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
The processes of RNA tertiary structure formation.
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained.
Sequential operating programs and data which instruct the functioning of a digital computer.
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Extracellular substance of bone tissue consisting of COLLAGEN fibers, ground substance, and inorganic crystalline minerals and salts.
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A member of the metalloproteinase family of enzymes that is principally responsible for cleaving FIBRILLAR COLLAGEN. It can degrade interstitial collagens, types I, II and III.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Compounds that inhibit the enzyme activity or activation of MATRIX METALLOPROTEINASES.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The posture of an individual lying face up.
Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.
Spectrophotometry in the infrared region, usually for the purpose of chemical analysis through measurement of absorption spectra associated with rotational and vibrational energy levels of molecules. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
The posture of an individual lying face down.
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The relationships of groups of organisms as reflected by their genetic makeup.
Computer-based representation of physical systems and phenomena such as chemical processes.
Ribonucleic acid that makes up the genetic material of viruses.
An extracellular endopeptidase of vertebrate tissues similar to MATRIX METALLOPROTEINASE 1. It digests PROTEOGLYCAN; FIBRONECTIN; COLLAGEN types III, IV, V, and IX, and activates procollagenase. (Enzyme Nomenclature, 1992)
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The rate dynamics in chemical or physical systems.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Proteins prepared by recombinant DNA technology.
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
Measurement of the intensity and quality of fluorescence.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
A non-aqueous co-solvent that serves as tool to study protein folding. It is also used in various pharmaceutical, chemical and engineering applications.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Proteins found in any species of bacterium.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A polypeptide substance comprising about one third of the total protein in mammalian organisms. It is the main constituent of SKIN; CONNECTIVE TISSUE; and the organic substance of bones (BONE AND BONES) and teeth (TOOTH).
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
The smallest member of the MATRIX METALLOPROTEINASES. It plays a role in tumor progression.
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC
A transmembrane domain-containing matrix metalloproteinase. It is synthesized as an inactive zymogen that is activated by the action of PROPROTEIN CONVERTASES such as FURIN. Matrix metalloproteinase 14 plays a direct role in the cleavage of proteins in the pericellular environment. In addition, it can function indirectly by enzymatically activating the proprotein form of MATRIX METALLOPROTEINASE 15.
A secreted matrix metalloproteinase that plays a physiological role in the degradation of extracellular matrix found in skeletal tissues. It is synthesized as an inactive precursor that is activated by the proteolytic cleavage of its N-terminal propeptide.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Established cell cultures that have the potential to propagate indefinitely.
Glycoproteins found on the surfaces of cells, particularly in fibrillar structures. The proteins are lost or reduced when these cells undergo viral or chemical transformation. They are highly susceptible to proteolysis and are substrates for activated blood coagulation factor VIII. The forms present in plasma are called cold-insoluble globulins.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A representation, generally small in scale, to show the structure, construction, or appearance of something. (From Random House Unabridged Dictionary, 2d ed)
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
Stable nitrogen atoms that have the same atomic number as the element nitrogen, but differ in atomic weight. N-15 is a stable nitrogen isotope.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
A group of pathogens comprising the smallest known agents of infectious disease. They are unencapsulated and are capable of replicating autonomously in susceptible cells. Positively identified viroids composed of single-stranded RNA have been isolated from higher plants, but the existence of DNA viroids pathogenic to animals is suspected.
Liquids that dissolve other substances (solutes), generally solids, without any change in chemical composition, as, water containing sugar. (Grant & Hackh's Chemical Dictionary, 5th ed)
A strong organic base existing primarily as guanidium ions at physiological pH. It is found in the urine as a normal product of protein metabolism. It is also used in laboratory research as a protein denaturant. (From Martindale, the Extra Pharmacopoeia, 30th ed and Merck Index, 12th ed) It is also used in the treatment of myasthenia and as a fluorescent probe in HPLC.
ENDOPEPTIDASES which use a metal such as ZINC in the catalytic mechanism.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
The thermodynamic interaction between a substance and WATER.
The sum of the weight of all the atoms in a molecule.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.
Matrix metalloproteinases that are associated with the CELL MEMBRANE, either through transmembrane domains or GLYCOSYLPHOSPHATIDYLINOSITOL ANCHORS. Membrane-type matrix metalloproteinases may act within the pericellular environment to influence the process of CELL MIGRATION.
An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.
Constituent of the 50S subunit of prokaryotic ribosomes containing about 120 nucleotides and 34 proteins. It is also a constituent of the 60S subunit of eukaryotic ribosomes. 5S rRNA is involved in initiation of polypeptide synthesis.
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Presence of warmth or heat or a temperature notably higher than an accustomed norm.
Proteins obtained from ESCHERICHIA COLI.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
Organic esters of sulfuric acid.
The position or attitude of the body.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A secreted matrix metalloproteinase which is highly expressed by MACROPHAGES where it may play a role in INFLAMMATION and WOUND HEALING.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
The portion of an interactive computer program that issues messages to and receives commands from a user.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
Elements of limited time intervals, contributing to particular results or situations.
Analysis of the intensity of Raman scattering of monochromatic light as a function of frequency of the scattered light.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
A class of organic compounds which contain an anilino (phenylamino) group linked to a salt or ester of naphthalenesulfonic acid. They are frequently used as fluorescent dyes and sulfhydryl reagents.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Deletion of sequences of nucleic acids from the genetic material of an individual.
Microscopy using an electron beam, instead of light, to visualize the sample, thereby allowing much greater magnification. The interactions of ELECTRONS with specimens are used to provide information about the fine structure of that specimen. In TRANSMISSION ELECTRON MICROSCOPY the reactions of the electrons that are transmitted through the specimen are imaged. In SCANNING ELECTRON MICROSCOPY an electron beam falls at a non-normal angle on the specimen and the image is derived from the reactions occurring above the plane of the specimen.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.
Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
Proteins associated with the inner surface of the lipid bilayer of the viral envelope. These proteins have been implicated in control of viral transcription and may possibly serve as the "glue" that binds the nucleocapsid to the appropriate membrane site during viral budding from the host cell.
The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.
The ability of a substance to be dissolved, i.e. to form a solution with another substance. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
The functional hereditary units of BACTERIA.
A codon that directs initiation of protein translation (TRANSLATION, GENETIC) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A member of the family of TISSUE INHIBITOR OF METALLOPROTEINASES. It is a N-glycosylated protein, molecular weight 28 kD, produced by a vast range of cell types and found in a variety of tissues and body fluids. It has been shown to suppress metastasis and inhibit tumor invasion in vitro.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
A subclass of matrix metalloproteinases that are secreted into the pericellular space.
The characteristic three-dimensional shape of a molecule.
Chemical groups containing the covalent disulfide bonds -S-S-. The sulfur atoms can be bound to inorganic or organic moieties.
A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
A family of secreted protease inhibitory proteins that regulates the activity of SECRETED MATRIX METALLOENDOPEPTIDASES. They play an important role in modulating the proteolysis of EXTRACELLULAR MATRIX, most notably during tissue remodeling and inflammatory processes.
The physical phenomena describing the structure and properties of atoms and molecules, and their reaction and interaction processes.
A compound formed in the liver from ammonia produced by the deamination of amino acids. It is the principal end product of protein catabolism and constitutes about one half of the total urinary solids.
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Proteins found in any species of virus.
The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
A computer architecture, implementable in either hardware or software, modeled after biological neural networks. Like the biological system in which the processing capability is a result of the interconnection strengths between arrays of nonlinear processing nodes, computerized neural networks, often called perceptrons or multilayer connectionist models, consist of neuron-like units. A homogeneous group of units makes up a layer. These networks are good at pattern recognition. They are adaptive, performing tasks by example, and thus are better for decision-making than are linear learning machines or cluster analysis. They do not require explicit programming.
Transport proteins that carry specific substances in the blood or across cell membranes.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
A genus of ciliate protozoa commonly used in genetic, cytological, and other research.
Glycoproteins which have a very high polysaccharide content.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.
An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.
Enzymes that catalyze the degradation of collagen by acting on the peptide bonds.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
The process of cleaving a chemical compound by the addition of a molecule of water.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
A member of the family of TISSUE INHIBITOR OF METALLOPROTEINASES. It is a 21-kDa nonglycosylated protein found in tissue fluid and is secreted as a complex with progelatinase A by human fibroblast and uncomplexed from alveolar macrophages. An overexpression of TIMP-2 has been shown to inhibit invasive and metastatic activity of tumor cells and decrease tumor growth in vivo.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes.
Large, noncollagenous glycoprotein with antigenic properties. It is localized in the basement membrane lamina lucida and functions to bind epithelial cells to the basement membrane. Evidence suggests that the protein plays a role in tumor invasion.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
Jones DT (September 1999). "Protein secondary structure prediction based on position-specific scoring matrices". J. Mol. Biol. ... Ouali M, King RD (June 2000). "Cascaded multiple classifiers for secondary structure prediction". Protein Sci. 9 (6): 1162-76. ... Cuff JA, Barton GJ (August 2000). "Application of multiple sequence alignment profiles to improve protein secondary structure ... Rost B (2001). "Review: protein secondary structure prediction continues to rise". J. Struct. Biol. 134 (2-3): 204-18. ...
"Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices" (PDF). Journal of Molecular Biology. 292 (2 ... PSIBLAST is used to find related sequences and to build a position-specific scoring matrix. This matrix is processed by an ... Secondary structure prediction involves a set of methods in bioinformatics that aim to predict the local secondary structures ... describe specific atomic positions in three-dimensional space, which are considered to be the tertiary structure. Secondary ...
Jones, David T. (1999). "Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices" (PDF). Journal of ... "Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: a prediction of the structure ... Predictions of protein secondary structure by Benner and colleagues achieved high accuracy. It became possible to model protein ... The use of multiple sequence information to predict secondary structure of proteins became popular as a result of the work of ...
Jones D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195- ... Structure prediction methods: secondary structure, solvent accessibility and membrane helices predicted by the PHD and PROF ... Biol., 322, 53-64 Liu J. and Rost,B. (2003) NORSp: predictions of long regions without regular secondary structure. Nucleic ... Methods Enzymol., 266, 525-539 Rost B. (2001) Protein secondary structure prediction continues to rise. J. Struct. Biol., 134, ...
"Prediction of disordered regions in proteins from position specific score matrices". Proteins: Structure, Function, and ... These alignments can also take into account patterns of predicted or known secondary structure elements and can be scored using ... released in June 2005 and uses a profile-profile alignment algorithm based on each protein's position-specific scoring matrix. ... The profile generated by PSI-BLAST is then processed by the neural network secondary structure prediction program PsiPred and ...
Position-specific scoring matrix (sequence context, also known as weight or scoring matrix) represents a conserved region in a ... Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the local secondary structures of ... Each matrix column represents the variation found in one column of the multiple sequence alignment. Position-specific scoring ... Matrix columns represent the amino acid variation found at one amino acid position in the aligned structures. Primary structure ...
Profiles are also known as Position Specific Scoring Matrices (PSSMs). In 1993, a probabilistic interpretation of profiles was ... giving rise to a model of the tRNA secondary structure. In 1970, Saul B. Needleman and Christian D. Wunsch published the first ... with known 3D structures. There have been a large number of diverse approaches to solve the structure prediction problem. In ... The 3D structures of molecules are of great importance to their functions in nature. Since structural prediction of large ...
Statistical Significance of Local Sequence Alignment Using Sequence-Specific and Position-Specific Substitution Matrices". IEEE ... Based on measures such as rigid-body root mean square distance, residue distances, local secondary structure, and surrounding ... The profile matrix for each conserved region is arranged like a scoring matrix but its frequency counts for each amino acid or ... DNA and RNA alignments may use a scoring matrix, but in practice often simply assign a positive match score, a negative ...
Atlas of Protein Sequence and Structure. 5 (3): 345-352. Eddy, SR (2004). "Where did the BLOSUM62 alignment score matrix come ... "A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence". Journal ... or for local sequence-structure contexts. These context-specific substitution matrices lead to generally improved alignment ... One PAM unit is defined as 1% of the amino acid positions that have been changed. To create a PAM1 substitution matrix, a group ...
... species are 139-142 nt long (Table 1) and share a common secondary structure consisting of two stem loops and a well ... and used those position weight matrices (PSWM) provided by RegulonDB ( We built PSWM for each ... All these sequences showed significant Infernal E-values (1.38e-33 - 1.05e-11) and bit-scores. In the case of S. meliloti a ... This characteristic sequence has been proposed as the specific binding site for the LysR-type proteins. All promoter regions of ...
The location of the secondary structures are also conserved. Pepsin (pH 1.3), Asp-N endopeptidase, N-terminal Glutamate and ... left in the table even though Homo sapiens and Macaca mulatta did not have significant scores above threshold for that position ... since it is needed for both the cell surface and extracellular matrix,it may explain CXorf26's high expression in nearly all ... of the endoplasmic reticulum and is initiated by the transfer of a xylose from UDP-xylose by xylosyltransferase to specific ...
... position-specific gap penalties and weight matrix choice". Nucleic Acids Res. 22 (22): 4673-80. doi:10.1093/nar/22.22.4673. PMC ... Most modern progressive methods modify their scoring function with a secondary weighting function that assigns scaling factors ... Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures ... The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global ...
A position weight matrix (PWM) contains log odds weights for computing a match score. A cutoff is needed to specify whether an ... Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular ... For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical ... There are two types of weight matrices. A position frequency matrix (PFM) records the position-dependent frequency of each ...
"SOSUI". Classification and Secondary Structure Prediction of Membrane Proteins. Mitaku Group. Xue Y, Ren J, Gao X, Jin C, Wen L ... that interact with PRP36 as predicted by the ElDorado tool from Genomatix-all shown factors received a minimum Matrix Sim score ... This promoter exists on the negative strand from position 7939226 to 7939826 and is 601 base pairs in length. The PRP36 ... Yao X (Sep 2008). "GPS 2.0, a tool to predict kinase-specific phosphorylation sites in hierarchy". Molecular & Cellular ...
The presumed structure of the c-terminal of the protein has been found to resemble that of the known secondary structure of ... NDUFAF5 is located on the p arm of Chromosome 20 in position 12.1 and spans 36,554 base pairs. The NDUFAF5 gene produces a 30 ... This gene encodes a mitochondrial protein that is associated with the matrix face of the mitochondrial inner membrane and is ... Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver ...
"CFSSP: Chou & Fasman Secondary Structure Prediction Server". Archived from the original on 9 August 2020. ... Casein kinase (CK1) phosphorylation site at position 335-341 aa. Two CK2 phosphorylation sites at positions 343-349 aa and 376- ... secondary DNA binding preference) Early B-cell factor 1 (Neuron specific olfactory factor) Nascent polypeptide-associated ... The top scoring (>88) miRNAs are hsa-miR-5197-3p, hsa-miR-4688, hsa-miR-3150a-3p, hsa-miR-16-5p, hsa-miR-195-5p, hsa-miR-15a-5p ...
... and DNA secondary structures affecting the fidelity of the sequence. Dye-terminator sequencing utilizes labelling of the chain ... covalently bound to a polyacrylamide matrix. Extension fragments are immobilized by the gel matrix, and excess primer, template ... These programs score the quality of each peak and remove low-quality base peaks (which are generally located at the ends of the ... Limitations include non-specific binding of the primer to the DNA, affecting accurate read-out of the DNA sequence, ...
Sequence alignment software Protein structure prediction Position-specific scoring matrix Multiple sequence alignment CASP - ... the addition of secondary structure predictions to MSAs, the extraction of alignments from program output, and the generation ... A position-specific scoring matrix (PSSM) profile contains for each position in the query sequence the similarity score for the ... "similarity scores". Because profiles contain much more information than a single sequence (e.g. the position-specific degree of ...
JASSA uses a scoring system based on a Position Frequency Matrix derived from the alignment of experimental SUMOylation sites ... The structure of human SUMO1 is depicted on the right. It shows SUMO1 as a globular protein with both ends of the amino acid ... Specific proteases mediate this procedure (SENP in human or Ulp1 and Ulp2 in yeast). Recombinant proteins expressed in E. coli ... identification of database hits matching the query sequence and representation of candidate sites within the secondary ...
... species are 99-121 nt long (Table 1) and share a well defined common secondary structure consisting of three stem ... and used those position weight matrices (PSWM) provided by RegulonDB ( We built PSWM for each ... specific probes for each sRNA could be designed which detected transcripts of different size and expression profiles. TAP-based ... H13 All these sequences showed significant bit scores and Infernal E-values (1.71e-28 - 2.03e-20). However, the plasmidic ...
... de novo protein structure prediction, and secondary structure prediction is available in the list of protein structure ... The structure of a protein is directly related to its function. The presence of certain chemical groups in specific locations ... Some validation strategies consist of calculating energy scores and comparing them with experimentally determined structures. ... A high quantity of amino acids allocated in no permissive positions of the chart is an indication of a low-quality modeling. A ...
Cut-out score - Cycle (music) - Cyclic form - Cyclic set - Cymbal D - D♭ - D♯ - D-sharp minor - D major - D minor - D-flat ... Fundamental structure - Furniture music - Futurism (music) G - G♭ - G♯ - G major - G minor - G-flat major - G-sharp major - G- ... Thumb position - Tie (music) - Tiento - Timbre - Timbre composition - Timeline of trends in Italian music - Time point - Time ... Generic and specific intervals - Genus (music) - German organ schools - Ghost note - Gigue - Giovane scuola - Glee Glissando - ...
"An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers". Human Molecular ... CONSENSUS secondary structure prediction". Retrieved 2020-04-29. "CFSSP: Chou & Fasman Secondary Structure ... This promoter region is on the minus (-) strand and has a start position of 1,137,965 and an end position of 1,139,325, making ... The majority of C7orf50 (isoform a) secondary structure is made up of alpha helices, with the remainder being small portions of ...
Knee injury and Osteoarthritis Outcome Score (KOOS) and Hip disability and Osteoarthritis Outcome Score (HOOS) surveys. ... For knee osteoarthritis in particular, increased risk was found among those who work in a kneeling or squatting position, ... They are also more expensive than non-specific NSAIDs. Benefits and risks vary in individuals and need consideration when ... However, during onset of osteoarthritis, the collagen matrix becomes more disorganized and there is a decrease in proteoglycan ...
... since the processes of mummification and fossilization heavily alter the structure of soft tissues in a way specific to the ... or of the primary versus secondary visual cortex), and to derive more specific information, such as the encephalization ... With the exception of the usually slice-based histology of the brain, neuroimaging data are generally stored as matrices of ... Miller, Michael I.; Younes, Laurent; Trouvé, Alain (2013-11-18). "Diffeomorphometry and geodesic positioning systems for human ...
"Figure S6: Predicted secondary structure of CoV-RMEN using CFSSP:Chou and Fasman secondary structure prediction server". doi: ... Zhang Y, Skolnick J (2005-04-11). "TM-align: a protein structure alignment algorithm based on the TM-score". Nucleic Acids ... f*The coordinates/positions are for GRCh38.p7. The clinical significance of SLC46A3 surrounds the protein's activity as a ... August 2007). "Liver-specific knockdown of JNK1 up-regulates proliferator-activated receptor gamma coactivator 1 beta and ...
The scores for each paired and unpaired residue explain likelihood for secondary structure formations. Production rules also ... By counting bases in single base positions and paired positions one obtains the frequencies of bases in loops and stems. For ... The weight of a specific parse tree in a WCFG is the product (or sum ) of all rule weights in the tree. Each rule weight is ... For unpaired bases a 4 X 4 mutation rate matrix is used that satisfies that the mutation flow from X to Y is reversible: P X r ...
"a structured, measured set of activities designed to produce a specific output for a particular customer or market. It implies ... In my management advisory activities I run into scores of these different programs all parading under the same name. Few are ... Order : It must consist of activities that are ordered according to their position in time and space (a sequence). ... as a flowchart of a sequence of activities with interleaving decision points or as a process matrix of a sequence of activities ...
The words in the catalogue were scored according to a two dimensional matrix taxonomy with orthogonal dimensions of affiliation ... obtainment of leadership positions) and not onto others or society at large. A study found that individuals who score low in ... Corry, N.; Merritt, R.D.; Mrug, S.; Pamp, B. (2008). "The factor structure of the Narcissistic Personality Inventory". Journal ... A more specific confound might also exist for dark triad traits and Machiavellianism in particular: individuals who are skilled ...
A data point is a variable with observed scores, like a variable containing the scores on a question or the number of times ... SEM-specific software[edit]. Several software packages exist for fitting structural equation models. LISREL was the first such ... In specifying pathways in a model, the modeler can posit two types of relationships: (1) free pathways, in which hypothesized ... Bentler, P.M. & Bonett, D.G. (1980), "Significance tests and goodness of fit in the analysis of covariance structures", ...
CHA2DS2-VASc score. Both the CHADS2 and the CHA2DS2-VASc score predict future stroke risk in people with A-fib with CHA2DS2- ... and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: a systematic analysis ... Secondary AF - occurs in the setting of a primary condition that may be the cause of the AF, such as acute myocardial ... The TEE has much better visualization of the left atrial appendage than transthoracic echocardiography.[65] This structure, ...
"AIA Statutory Matrix on the Legal Relationships Between the Professions of Architecture and Engineering" (PDF). AIA Website. ... The word engineer has a broad sense and can refer to multiple different jobs associated with engineering.[51] Specific titles, ... Structures subject to building codes are not covered by an industrial exemption, though small residential buildings often do ... R.Eng standing for registered engineer in Kenya (Holders of five years of post-secondary engineering education and four years ...
... primary and secondary structure of the replicase gene". Nature. 260 (5551): 500-7. Bibcode:1976Natur.260..500F. doi:10.1038/ ... This method made it susceptible to sequence-specific bias or loss of specific sequences. Because the technology was so complex ... Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, or MALDI-TOF MS, has specifically been ... Phil Green and Brent Ewing of the University of Washington described their phred quality score for sequencer data analysis in ...
Of the above, hypodense (dark) structures can indicate edema and infarction, hyperdense (bright) structures indicate ... A specific measure, termed the computed tomography dose index (CTDI), is commonly used as an estimate of the radiation absorbed ... Pixel is a two dimensional unit based on the matrix size and the field of view. When the CT slice thickness is also factored in ... Computed tomography operates by using an X-ray generator that rotates around the object; X-ray detectors are positioned on the ...
The specific problem is: to update the 2006 authoritative summary of uses, and to sift through the remaining weak description ... With secondary sources, it is often you find data that is similar to a process but not exact (e.g. data from a different ... It allows studies to aggregate impact scores into a single indicator for comparison.[30] Weighting is highly subjective and as ... The data is typically detailed in charts and requires a structured approach due to its complex nature.[26] ...
A number of risk scores exist to predict bleeding in people using warfarin and similar anticoagulants. A commonly used score ( ... Warfarin is used to decrease the tendency for thrombosis or as secondary prophylaxis (prevention of further episodes) in those ... No specific treatment is available, but some modalities are under investigation.[45] ... or matrix Gla protein, may also be affected. The precursors of these factors require gamma carboxylation of their glutamic acid ...
Stefflre, V. (1968). Market Structure Studies: New products for old markets and new markets (foreign) for old products. New ... Those who score high on brand-consciousness tend to believe that the higher prices are an indicator of quality and exhibit a ... Secondary groups: groups such as clubs, societies, sports teams, political parties, religions that align with a person's ideas ... Specific brand names enter the consumer's consideration set based on the extent to which they satisfy the consumer's purchasing ...
Tortora C, Meazzini MC, Garattini G, Brusati R (March 2008). "Prevalence of abnormalities in dental structure, position and ... There are three types of dentin, primary, secondary and tertiary.[18] Secondary dentin is a layer of dentin produced after root ... It is also useful to note that patients with a cleft lip and palate automatically score a 5 on the IOTN ( index for orthodontic ... There are several different notation systems to refer to a specific tooth. The three most common systems are the FDI World ...
Some role-playing games also give the player specific skill points, which can be used to unlock a new skill or improve an ... The world of Paradise Cracked was largely influenced by such movies as Matrix, Blade Runner and Ghost in the Shell, as well as ... Players must acquire enough power to overcome a major challenge in order to progress to the next area, and this structure can ... For instance, The Elder Scrolls IV: Oblivion, which is the only Western RPG to have been awarded a near-perfect score by ...
... scoring only 1.5 out of 5 privacy points. According to the annual Democracy Matrix, which is published by the University of ... Human Diversity site-research and study source directed at secondary and post-secondary students Freedom in the World 2006: ... The vast majority of executions are carried out by state governments, largely as a result of the federal political structure of ... Treaties regarding human rights, which create a duty to refrain from acting in a particular manner or confer specific rights, ...
... which was a civil-service position. Although it recognized the importance of her work, the position still provided no salary. ... The real utility of modules is that the kinds of modules that exist and their interactions, reveal the structure of the ring in ... For illustration, a system of equations often can be written in the form M v = 0 where a matrix (or linear transform) M ( ... In the spring of 1900, she took the examination for teachers of these languages and received an overall score of sehr gut (very ...
Her mecha is equipped with rocket Boosters for short bursts of flight, as well as a Defense Matrix that allows it to shoot ... Since the cooldown for his Swift Strike resets upon scoring a kill, it is best used as a finishing move. Genji's Deflect ... His main weapon is a Medic SMG, a submachine gun alongside a secondary Biotic Launcher that fires projectiles that heal allies ... While some characters function best when paired with specific teammates, Genji works best in isolation. Genji is strong against ...
... using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores ... To infer the specifics of particular events, genome spectral or subtree pruning and regraft methods are required. In order to ... In another study, the context was used as a secondary indicator, after removal of genes which are strongly thought to be native ... Artificial chimeric genomes can be obtained by inserting known foreign genes into random positions of a host genome. The donor ...
On February 28, 2019, Richard Plepler stepped down from his position as CEO of Home Box Office, Inc., after a collective 27- ... Biondi's replacement, Michael J. Fuchs, structured some of the subsequent deals as non-exclusive to allow HBO to divert more ... HBO had already placed resources to grow its secondary, lower-cost "maxi-pay" service, Cinemax, which launched in August 1980. ... The twelve-note musical signature of the sequence's orchestral fanfare-originally composed for Score Productions by Ferdinand ...
"The entire structure is set up to provide areas where you can input your own information. It supports all file types, including ... As the ALT-J editor Jane Seale notes, "the purpose of the review is to make sense of the current position in which the field ... Mitre Matrix, 8(4) - ERIC Document ED121328 Robert H'obbes' Zakon (2005-08-28). "Hobbes' Internet Timeline v8.1". Retrieved ... In datacloud,Datacloud: Toward a New Theory of Online Work, Johndan Johnson-Eilola describes a specific computer-supported ...
He later played secondary roles in several other formative American noirs. Although modestly budgeted, at the high end of the B ... For specific production circumstances, see Brady, Frank, Citizen Welles: A Biography of Orson Welles (1989), pp. 395-404, 378- ... The Animatrix (2003), based on and set within the world of The Matrix film trilogy, contains an anime short film in classic ... Perhaps no director better displayed that spirit than the German-born Robert Siodmak, who had already made a score of films ...
During the May 2011 sweeps period, the 10 p.m. news regained its position as the market's #1 late newscast in total viewers and ... In 1950, WFAA switched its primary affiliation to NBC, and also affiliated with ABC on a secondary basis. DuMont shut down in ... Once the corporate separation was finalized on June 29, 2015, WFAA became part of Tegna, which was structured as the legal ... Ed Bark (May 26, 2011). "Fox4 paces May "sweeps" local newscast ratings, with WFAA8 also scoring points (with some sleight-of- ...
The term matrix was coined by James Joseph Sylvester, a major contributor to the theory of determinants. It is difficult to ... The permanent structure sustained three fires but as an institution lasted a full century, with Andrew Ducrow and William Batty ... She was the first, and last, woman to score the highest on the Tripos. While women were not welcomed in the world of medicine, ... In prose, the novel rose from a position of relative neglect during the 1830s to become the leading literary genre by the end ...
Gabriel's Secondary School St. Hilda's Secondary School St. Joseph's Institution, Singapore St. Margaret's Secondary School St ... Marina Bay The Sam Willows The Sam Willows discography The Scarlet Singapore The Scent of the Gods The Score (Singaporean TV ... Especially Women and Children Protocol to the Convention on International Interests in Mobile Equipment on Matters specific to ... Police Technology Department Political positions of Lee Kuan Yew Politics of Singapore Pollutant Standards Index Polytremis ...
1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292(2):195-202. ... The model was manually refined, including corrections of the alignment using the PSI-PRED (67) secondary structure predictions ... 2012) Selective and specific inhibition of the plasmodium falciparum lysyl-tRNA synthetase by the fungal secondary metabolite ... Schrödingers GlideScore scoring function was used to score and rank the predicted docking poses. ...
Here we present the atomic structure of the portal protein of Epstein-Barr virus, solved by cryo-electron microscopy at 3.5 Å ... Here the authors describe a high-resolution atomic structure of the EBV portal, which serves as the entrance and exit pore for ... Here the authors describe a high-resolution atomic structure of the EBV portal, which serves as the entrance and exit pore for ... Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202 ( ...
The structures provide insights into the organization of subunits within complexes and the interactions between the complexes. ... Two studies in this issue of Nature report cryo-electron microscopy structures of the supercomplex consisting of complex I, the ... cryo-electron microscopy structures of mammalian (sheep) respirasomes are presented. Mitochondrial electron transport chain ... Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202 ( ...
Jones, D.: Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292 ... Sander, C., Schneider, R.: Database of homology-derived protein structures. Proteins 9 (1991) 56-68CrossRefGoogle Scholar ... CN is a kind of simplified profile of the 3D structure of a protein. Two kinds of experiments are described, the first of them ... Protein Chain Minimum Description Length Protein Structure Prediction Input Attribute Amino Acid Type These keywords were added ...
Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292(2):195-202. ... Strom MS, Lory S (1993) Structure-function and biogenesis of the type-IV pili. Annu Rev Microbiol 47:565-596. doi: 10.1146/ ... Wolodko WT, Fraser ME, James MNG, Bridger WA (1994) The crystal-structure of cussinyl-CoA synthetase from Escherichia coli at ... Alexeev D, Alexeeva M, Baxter RL, Campopiano DJ, Webster SP, Sawyer L (1998) The crystal structure of 8-amino-7-oxononanoate ...
Most notably there is a region of potential T cell cross-reactivity within the SARS-CoV-2 N protein position 102-110 amino ... Most notably there is a region of potential T cell cross reactivity within the SARS-CoV-2 N protein position 102-110 amino ... Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 292(2):195-202. doi: ... identify CD4+ T cell allele-specific epitopes encompassed in the sequences we identify from positions 213-238 to 293-320 as ...
Protein secondary structure prediction based on position-specific scoring matrices. J. mol. Biol., 292: 195-202. KISSELEVA, M.V ... protein structure prediction), which determine protein secondary structure prediction (Jones, 1999). Figure 1 summarizes ... Afterwords; effect on the protein secondary structure, arisen due to single amino acid substitution, determined 8 nsSNPs (out ... of SNP###morphism###coordi-###substituted###secondary value###secondary###value ###nates###amino acid###structure###structure ...
Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202. ... and a precomputed position-specific scoring matrix. The query sequence and the position-specific scoring matrix are both ... The overlap between the secondary structure prediction by PSIPRED (59) and the known structures of PP2C-type protein ... Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in ...
Additionally, the analysis of the structure and immunogenicity of the generated rCjaAD hybrid protein showed that the CjaA ... We showed that specific rabbit anti-rCjaAD serum reacted strongly with both CjaA and CjaD produced by a wild type Campylobacter ... We showed that specific rabbit anti-rCjaAD serum reacted strongly with both CjaA and CjaD produced by a wild type Campylobacter ... Jones, D. T. (1999b). Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, ...
1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202. ... The secondary structure states of all residues in a solved structure or a good quality comparative model were assigned by the ... Secondary Structural Elements Involved in Modification Of Substrate Proteins. To gain insight into what secondary structure ... defined as a model being evaluated with a GA341 score of , 0.8 (28) comparative model in ModBase (29)), secondary structure ...
Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202. ... E) Secondary structure prediction of ILDR2 IgV domain and β-strand organization. Predicted β-strands are marked by the letters ... Ig domain identification was performed using InterProScan (18). Secondary structures were predicted using PSIPRED (19) and ... For Ag-specific T cell activation, naive CD4+ T cells were isolated from spleens of DO11.10 mice (transgenic for an OVA323-339- ...
Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. We achieved ,svg ... matrix(.012,-0,0,-.012,22.62,15.475),,use xlink:href=#x74/,,/g,,g transform=matrix(.012,-0,0,-.012,26.308,15.475),,path id ... On average 25% of amino acids in protein structures are located in ,i ,β,/i,-turns. It is very important to develope an ... matrix(.012,-0,0,-.012,31.591,15.475),,path id=x6C d=M238 0h-223v26q48 5 60 17t12 61v473q0 50 -10.5 60.5t-58.5 15.5v24q73 8 ...
Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and ... Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding ... Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202. * ... while PoPS relies on a position-specific scoring matrix (PSSM) based on amino acid frequency to build predictive models [32]. ...
Jones DT (September 1999). "Protein secondary structure prediction based on position-specific scoring matrices". J. Mol. Biol. ... Ouali M, King RD (June 2000). "Cascaded multiple classifiers for secondary structure prediction". Protein Sci. 9 (6): 1162-76. ... Cuff JA, Barton GJ (August 2000). "Application of multiple sequence alignment profiles to improve protein secondary structure ... Rost B (2001). "Review: protein secondary structure prediction continues to rise". J. Struct. Biol. 134 (2-3): 204-18. ...
... applies a maximum entropy approach to infer evolutionary covariation in pairs of sequence positions within a protein family and ... We use this technique to predict previously unknown 3D structures for 11 transmembrane proteins (with up to 14 helices) from ... We benchmark the approach with blinded de novo computation of known transmembrane protein structures from 23 families, ... Protein secondary structure prediction based on position-specific scoring matrices.. *David T. Jones ...
Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202 (1999).. ... 1) Secondary structures. We ran a local psipred on the sequence and enforced secondary structure at an accuracy level between ... For example, MELD can be directed to "make a good hydrophobic core" or "make secondary structures consistent with Web server ... We based this on secondary structure predictions. We never applied restraints between residues that belong to the same strand. ...
Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202 (1999). doi: ... Crystal structures of nucleosome core particles containing the 601 strong positioning sequence. J. Mol. Biol. 403, 1-10 (2010 ... S7). The final structure of the CENP-A nucleosome core is similar to the crystal structure of the free CENP-A nucleosome [ ... Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins ...
"Protein Secondary Structure Prediction Based on Position-specific Scoring Matrices" (PDF). Journal of Molecular Biology. 292 (2 ... PSIBLAST is used to find related sequences and to build a position-specific scoring matrix. This matrix is processed by an ... Secondary structure prediction involves a set of methods in bioinformatics that aim to predict the local secondary structures ... describe specific atomic positions in three-dimensional space, which are considered to be the tertiary structure. Secondary ...
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292:195-202. doi:10.1006/jmbi. ... All positions containing gaps and missing data were removed. There were a total of 433 positions in the final data set. ... The structure-based cladogram was derived from sequence and structural alignments of the predicted tertiary structures of ... K) Structure-based cladogram derived from sequence and structural alignments of the predicted tertiary structures of multiple ...
... features extracted from the Position-Specific Scoring Matrix (PSSM). More specifically, the PSSMs are generated using the ... D. T. Jones, "Protein secondary structure prediction based on position-specific scoring matrices," Journal of Molecular Biology ... Position-Specific Scoring Matrix (PSSM). Position-Specific Scoring Matrix is first used in the detection of distantly related ... are constructed as a sparse rotation matrix , which is expressed as follows:. ...
Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202. ... We predicted the secondary protein structures for these novel or unidentified proteins. Using a protein secondary structure ... is identified at positions 99529 to 100248 in the genome, where it is situated at the position 277 bp upstream of the start ... Structure and function of the radical enzyme ribonucleotides reductase. Prog. Biophys. Mol. Biol. 77:177-268. ...
SWISS-MODEL is a fully automated protein structure homology-modelling server. The purpose of this server is to make protein ... Jones, D. T. (1999). "Protein secondary structure prediction based on position-specific scoring matrices." J Mol Biol 292(2): ... Mariani, V., Biasini, M., Barbato, A., Schwede, T. lDDT: a local superposition-free score for comparing protein structures and ... Kabsch, W. and C. Sander (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and ...
Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202 (1999). doi: ... We introduced Cys at membrane-facing positions as well as pore-facing positions of a Cys-free Tom40 variant (8). Cross-linked ... Structure of the cytosolic domain of TOM5, a mitochondrial import protein. FEBS Lett. 468, 101-104 (2000). doi:10.1016/S0014- ... Cryo-electron microscopy structure of a yeast mitochondrial preprotein translocase. J. Mol. Biol. 383, 1049-1057 (2008). doi: ...
1999b) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195-202. ... Supplemental Figure S1. Predicted secondary structure elements of the Gα regions of the XLGs. ... 5) upon insertion of the NmVenus210 fragment into a position analogous to the αB-αC loop insertion, a position that also ... and the conserved secondary structure patterning of the XLGs and GPA1 is evident when the Phyre2 data are superimposed over an ...
Jones, D.T. (1999). Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195- ... Protein Structure Analysis. Protein secondary structure prediction was performed with PSIpred version 2.0 (Jones, 1999). ... position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680. ... Based on the position on the tree and the presence of class-specific signatures, genes were named according to the proposed ...
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999;292(2):195-202. ... Crystal structure of a gammadelta T-cell receptor specific for the human MHC class I homolog MICA. Proc Natl Acad Sci U S A. ... Global alignments in protein secondary structure prediction and 3D visualization. Global alignment of the target and template ... Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features ...
Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol.292:195-202. ... 1B, both proteins present a mixture of secondary structures, as none of the spectra showed a flat line, characteristic of the ... Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network ... The estimation of the secondary structure content resulted in 37% and 26% α helix and β strands, respectively, for both ...
... become an area of active research as witnessed in the 6th experiment on Critical Assessment of Techniques for Protein Structure ... Jones DT: Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292: 195-202. ... the 20-column position-specific scoring matrix (PSSM) and the last 2 columns from the profile (i.e. information per position ... Jones DT, Ward JJ: Prediction of disordered regions in proteins from position specific score matrices. Proteins 2003, 53(Suppl ...
CRNPRED achieves, on average per chain, Q3 = 81% for secondary structure prediction, and correlation coefficients of 0.75 and ... We implemented a program CRNPRED which predicts secondary structures, contact numbers and residue-wise contact orders. This ... Unlike most conventional one-dimensional structure prediction methods which are based on local windows of an amino acid ... numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the sequence-structure ...
Protein secondary structure prediction based on position-specific scoring matrices. Jones, DT ... Application of multiple sequence alignment profiles to improve protein secondary structure prediction ... The structure of coxsackievirus B3 at 3.5 A resolution. Muckelbauer, JK; Kremer, M; Minor, I; Diana, G; Dutko, FJ; Groarke, J; ... Three-dimensional structure of Theiler murine encephalomyelitis virus (BeAn strain). Luo, M; He, C; Toth, KS; Zhang, CX; Lipton ...
  • In this study, a novel predictor was designed using the Rotation Forest (RF) algorithm combined with Autocovariance (AC) features extracted from the Position-Specific Scoring Matrix (PSSM). (
  • Almost all the modern predictors are based on position-specific scoring matrices (PSSM) and some kind of machine learning techniques such as neural networks or support vector machines. (
  • this list allows the user to choose a database of sequences for generating the position specific scoring matrix (PSSM) with the program PSI-BLAST. (
  • A different amino acid composition based Support Vector Machines models was developed, including the evolutionary profiles in the form position-specific scoring matrix (PSSM). (
  • Recently, it has observed that the use of evolutionary profile in the form of a position-specific scoring matrix (PSSM) predicted various functional proteins with a higher accuracy [ 16 , 17 ]. (
  • The difference between current and previous study reflected that PSSM and Hybrid approach, confusion matrix analysis, prediction score graphs, and ROC analysis has been added as extra features. (
  • CRNPRED uses a position-specific scoring matrix (PSSM) generated by PSI-BLAST as its input, and based on the PSSM, a machine-learning method called Critical Random Network (CRN) is applied. (
  • Generates a PSSM (Position specific scoring matrix) from the input alignment using csbuild to add pseudo-counts. (
  • The fragment picker picks both 3mers and 9mers based on similarity to the PSSM and secondary structure prediction. (
  • Position specific scoring matrix (PSSM) based on PSIBLAST shows evolutionary information and has made the most significant improvements in protein secondary structure prediction. (
  • Using amino acid composition (AAC), position-specific scoring matrix (PSSM) and N-terminal signal peptides, two different substitution models are firstly constructed to transform protein sequences into numerical vectors. (
  • In this study, an ensemble method is presented to predict antioxidant proteins with hybrid features, incorporating SSI Secondary Structure Information, PSSM Position Specific Scoring Matrix, RSA Relative Solvent Accessibility, and CTD Composition, Transition, Distribution. (
  • To consider also evolutionary information we created different PSSM matrices. (
  • Just as BLOSUM, the PSSM has positive and negative integer values as scores. (
  • A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. (
  • Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. (
  • Following recent research in this area, we propose a new machine learning system that is based on combining several protein descriptors extracted from different protein representations, such as position specific scoring matrix (PSSM), the amino-acid sequence, and secondary structural sequences. (
  • Consequently, this increase widens sequence-structure gap rapidly [ 1 , 2 ]. (
  • These levels are primary structure which refers to amino acid linear sequence of the polypeptide, secondary structure, which is defined by the patterns of hydrogen bonds between backbone amide and carboxyl groups, tertiary structure, which is the three-dimensional structure of a single protein molecule, and quaternary structure, which is a larger assembly of several protein molecules or polypeptide chains. (
  • PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database) with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. (
  • Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. (
  • Groups are given a protein sequence, with the structure blinded, asked to predict the three-dimensional structure in a fixed time frame (typically 3 weeks), and then evaluated when the structure is known. (
  • Now that the complete sequence of the nuclear genome of Arabidopsis is available ( Arabidopsis Genome Initiative, 2000 ), it is possible to scan an entire plant genome for all of these core cell cycle genes and determine their numbers, positions on the chromosomes, and phylogenetic relationships. (
  • Due to the functional importance of intrinsically disordered proteins or protein regions, prediction of intrinsic protein disorder from amino acid sequence has become an area of active research as witnessed in the 6th experiment on Critical Assessment of Techniques for Protein Structure Prediction (CASP6). (
  • One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the sequence-structure relationship. (
  • Unlike most conventional one-dimensional structure prediction methods which are based on local windows of an amino acid sequence, CRNPRED takes into account the whole sequence. (
  • 1D structures are not only useful for 3D structure predictions, but also helpful for intuitive understanding of the correspondence between the protein structure and its amino acid sequence due to the residue-wise characteristics of 1D structures. (
  • They can be used either as sequence-to-structure classifier, structure-to-structure classifier, or both. (
  • This paper addresses the problem of post-processing the outputs of multi-class support vector machines used as sequence-to-structure classifiers with a structure-to-structure classifier estimating the class posterior probabilities. (
  • To aid in the generalization of these results, we present here a comprehensive sequence alignment of all known prokaryotic and eukaryotic NSS proteins, based on the crystal structure of the leucine transporter from Aquifex aeolicus (LeuT). (
  • 13] J. D. Thompson, D. G. Higgins, and T. J. Gibson, "CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice," Nucleic Acids Research, Vol.22, pp. 4673-4680, 1994. (
  • The aim of Betaturns server is to predict different types of turns such as Types I, II, IV, VIII and non-specific in a given amino acid sequence. (
  • for each position of the sequence, each amino-acid of the multiple aligments possessing at least this PSI-BLAST threshold is taken into account for evaluating the score. (
  • Protein fold recognition using sequence profile searches frequently allows prediction of the structure and biochemical mechanisms of proteins with an important biological function but unknown biochemical activity. (
  • We employ sequence profile analysis to show that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. (
  • Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). (
  • It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). (
  • Analysis of the primary sequence and predicted structure of the 134R protein of Yaba-like disease virus (Y134R) indicated that it is similar to cellular proteins of the IL-10 family, specifically IL-19, IL-20 and IL-24. (
  • While above methods predict backbone structure at low-moderate resolution, we plan to develop a high resolution ANN contact prediction, from protein sequence only. (
  • Most prominent among such interaction motives is the leucine zipper - a recurring sequence pattern with Leucine in every 7th position - which is frequently observed in helix-helix interfaces. (
  • This and similar interaction motifs should be detectable from two stretches of amino acid sequence, since the well-defined interaction patterns require specific amino acid sequences in order to be possible. (
  • Given a sequence, MODPEP builds the peptide 3D structure from scratch by assembling amino acids or helix fragments based on constructed rotamer and helix libraries. (
  • These discriminative features include protein evolutionary information, predicted protein secondary structure, native disorder, physicochemical propensities and several sequence-based structural descriptors of residues. (
  • As a result of the completion of whole-genome sequencing projects, the sequence-structure gap is rapidly increasing. (
  • The page displays (from top to bottom) the input sequence, the secondary structure predicted with PSI-PRED (1), the fold type predicted by PFRES (23), the structural class predicted by SCEC (17), the secondary structure contents predicted with PSSC-core (9), and the cross-evaluation results. (
  • Therefore, adenovirus type 5 seems to contain sequence- or locus-specific DNA generic cialis tadalafil binding proteins within the virion. (
  • Additional calculations are performed including the search for similarities within or among genus, the search for signal sequence or transmembrane segments, predicted secondary structure and disulfide bonds, and the search for homologs with a known 3D structure in the Protein Databank . (
  • Therefore, although the sequence of GlSec61α is least conserved amongst all the orthologues considered in this study, secondary structure predictions indicate that it is likely to adopt a similar structure. (
  • CRNPRED is a web-based service that predicts one-dimensional (1D) protein structures including secondary structures, contact numbers, and residue-wise contact orders from amino acid sequence. (
  • P_H , P_E , and P_C mean the probability of finding helix (H), strand (E) and coil (C) structures at each sequence position. (
  • Studies show that certain sequence preferences influence calpain substrate recognition, and some properties of amino acids have been related successfully to substrate specificity and to the calpains' 3D structure. (
  • The full spectrum of this substrate specificity, however, has not been clarified using standard sequence analysis algorithms, e.g., the position-specific scoring-matrix method. (
  • The template resolution of different crystal structures ranged from 3.8 - 4.1 Å and the sequence identity between templates and human ABCC5 are in range 20.7% - 22.8%, clearly implying that the ABCC5 homology models has elements of uncertainty. (
  • Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. (
  • CRISPR-Cas systems can cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA) and the source of the Cas9 protein. (
  • Therefore, bioinformatics analysis and abinitio 3-D modelling of the protein sequence was performed using various computational analysis tools that suggest a helical organization for the protein with four transmembrane α-helices giving rise to a unique 3-D structure. (
  • Since the primary sequence conservation within and between the two families is relatively low, we explored the potential structural conservation between V4R and Bet3 using the available high resolution crystal structures of Bet3 family proteins. (
  • In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. (
  • Revealing the evolution and genetic diversity of sequences and organisms Identification of molecular structure from sequence alone In chemistry, sequence analysis comprises techniques used to determine the sequence of a polymer formed of several monomers. (
  • In sociology, sequence methods are increasingly used to study life-course and career trajectories, patterns of organizational and national development, conversation and interaction structure, and the problem of work/family synchrony. (
  • Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the local secondary structures of proteins based only on knowledge of their amino acid sequence. (
  • Single-sequence algorithms for protein secondary structure prediction are important because a significant percentage of the proteins identified in genome sequencing projects have no detectable sequence similarity to any known protein. (
  • prophecy generates for an input sequence alignment a simple frequency matrix (for use by profit) or a position specific weighted profile using either the Gribskov (1) or Henikoff (2) method (for use by prophet). (
  • The Gribskov scoring scheme is based on a notion of distance between a sequence and an ancestral or generalized sequence. (
  • For Henikoff it is based on weights of the diversity observed at each position in the alignment, rather than on a sequence distance measure. (
  • TTD was known to be one of the most popular pharmaceutical databases around the world, and included the links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, and clinical development status. (
  • Sequence Based Prediction of Antioxidant Proteins Using a Classifier Selection Strategy - Descarga este documento en PDF. (
  • Relatively high sequence conservation between plant CESAs allowed mapping of known mutations and two previously undescribed mutations that perturb cellulose synthesis in Arabidopsis thaliana to their analogous positions in the modeled structure. (
  • On the contrary, with the advances of bio-techniques in the past decade, the primary structure, i.e., the sequence of the protein in amino acids, can be found by high-throughput methods. (
  • So it is desirable that the protein structure can be inferred simply from the protein sequence. (
  • Using this primary sequence alignment, the tertiary structure of the core domain of lac repressor was modeled using the structures of the sugar binding proteins as templates. (
  • The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. (
  • The analysis showed 1) that escape mutations in the flavivirus envelope protein are variable residues by our criteria and 2) two escape mutants found at the same position in many flaviviruses sit above clusters of conserved residues from different regions of the linear sequence. (
  • Because of the availability of amino acid sequences generated in the post-genomic age, it is possible to predict an unknown protein's structural class using machine learning methods given a protein's amino-acid sequence and/or its secondary structural elements. (
  • One hidden layer for non-linear 2-class pattern classification w, More Complex NN Structure: PHD Multiple sequence Alignment, it is a way to compare multiple sequence, the result is called alignment profile. (
  • 12/11/2001 Sequence alignment (SA) of DNA, RNA and protein primary structure forms an integral, if not the most important part of bioinformatics. (
  • We use this technique to predict previously unknown 3D structures for 11 transmembrane proteins (with up to 14 helices) from their sequences alone. (
  • Important similarities and differences among the sequences of NSS proteins in regions likely to determine selectivity in substrate binding and mechanisms of transport regulation are discussed in the context of the LeuT structure and the alignment. (
  • The principle idea is to expand 1-D information of protein sequences by incorporating predicted secondary structure and solvent accessibility states of each amino acid. (
  • The resulting 'generalized sequences' are aligned with similarly expanded ('generalized') position specific scoring matrices. (
  • alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. (
  • BLAST against the PDB , in order to find structures homologous to peptide sequences. (
  • Widely used methods for protein domain assignment are: (i) based on three-dimensional structure that include independently foldable units or structural domains and (ii) based on conserved primary sequences that include independently evolving units or conserved functional domains. (
  • Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. (
  • The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. (
  • Prediction of protein structure from amino-acid sequences has been one of the most challenging problems in computational structural biology for many years [ 1 , 2 ]. (
  • The first two approaches build protein models by aligning query sequences onto solved template structures. (
  • Faber S, Wilcox K (1986) Association of the herpes simplex virus regulatory protein ICP4 with specific nucleotide sequences in DNA. (
  • Machine learning has also elucidated information about the properties of calpains' substrate specificities, including a preference for sequences over secondary structures and the existence of a substrate specificity difference between two similar conventional calpains, which has never been indicated biochemically. (
  • The two sequences were analyzed using the fold recognition meta-server PHYRE [ 10 ], which generated a 50-70% confidence hit to Bet3 family proteins structures. (
  • To obtain structure models of the I. hospitalis and N. equitans V4R domains, the sequences were first aligned by hand to those of TPC6 (PDB:2bjn) and BET3 (PDB:1wc8) which served as templates. (
  • In 1969 the analysis of sequences of transfer RNAs were used to infer residue interactions from correlated changes in the nucleotide sequences, giving rise to a model of the tRNA secondary structure. (
  • Relationships between these sequences are usually discovered by aligning them together and assigning this alignment a score. (
  • Algorithms of another type are explicitly using sequences of homologous proteins, which often have similar structures. (
  • For example, transcription factors bind to specific DNA sequences in promoters to activate gene expression [ 1 ]. (
  • The CPS of Kp13 probably includes L-rhamnose and D-galacturonate in its structure, among other residues. (
  • In addition, adaptive selection of specific residues in the ectodomains enhances mammalian Pcdh diversity [ 5 ]. (
  • Mutagenesis studies verified that both of these proteins are K63- polyubiquitinated at specific Lysine residues, K485 in TrkA and K19 in NRIF. (
  • The top ranked ABBC5 model was based on template 4Q9H that had 91.2% of residues in allowed regions as revealed by PROCHECK-NMR and the QMEAN score was 0.54 which indicated a reliable model. (
  • The columns represent amino acid counts for the amino acid residues from A to Z. The rows represent the alignment positions from 1->n. (
  • The core domain (residues 62-323) of the regulatory protein lac repressor has been aligned to several sugar binding proteins of known structure. (
  • This approach provides an effective means to visualize the core domain of the lac repressor and to interpret the mutational data for specific residues. (
  • Critical functional residues, like active site residues, have high positive scores. (
  • The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. (
  • Mapping of known Cd 2+ block sites and conserved protonatable residues onto the structure delineates two noncontiguous pathways across the complex, connecting two adjacent proton-binding sites in the c -ring to the space on either side of the membrane. (
  • Stereophysicochemical variability plots (SVPs), 3-D images of protein structures colored according to variability, as determined by our PCPMer program, were used to visualize residues conserved in their p hysical c hemical p roperties (PCPs) near escape mutant positions. (
  • Here, we present a method that can be used to interpret escape mutations in a different way, by detecting conserved residues that are "cloaked" by these variable positions. (
  • These invariant residues are more likely to be the important targets of neutralizing antibodies the escape mutants, which typically occur at variable positions. (
  • We find that the escape mutants found in the same position in several different flaviviruses lie above highly conserved, known functional areas of the viral proteins, such as the receptor binding site, and disulfide bonded residues. (
  • The correlation of predicted secondary structure and solvent accessibility states is in most cases higher than between predicted and observed states (Przybylski & Rost 2004). (
  • The prediction of solvent accessibility could provide valuable clues for analyzing protein structure and functions, such as protein 3-Dimensional structure and B-cell epitope prediction. (
  • To fully decipher the protein-protein interaction process, an initial but crucial step is to calculate the protein solvent accessibility, especially when the tertiary structure of the protein is unknown. (
  • To meet the need of protein tertiary structure prediction, which requires a numerical measure of protein solvent accessibility, recent studies mainly focused on predicting the real values of the solvent accessibility. (
  • they include secondary structure (1-5), secondary structure content (6-9), structural class (10-17), fold type (18-25), relative solvent accessibility (26-32), contact order and number (33-37), and residue depth (38). (
  • From an evolutionary point of view, this core cell cycle gene catalog would be extremely interesting because it allows us to determine which processes are specific to plants and which are conserved among all eukaryotes. (
  • These features included evolutionary conservation profile, secondary structure motifs, and physicochemical properties. (
  • No X-ray crystal structure of ABCC5 has been reported, but molecular models of ABCC5 may be constructed by homology using a known 3D crystal structure of an evolutionary related protein as a template. (
  • Many machine learning methods have been developed to predict protein secondary structure, and exhibit good performance by exploiting evolutionary information, as well as statistic information about amino acid subsequences. (
  • Structural characterization of the DNA-binding domains of various response regulators revealed several variations on the common helix-turn-helix (HTH) theme, exemplified by the NarL-type, OmpR-type "winged helix," Spo0A-type, and Fis-like structures ( 12 , 78 , 79 , 87 , 88 , 100 ). (
  • Kopp, J., Schwede, T. The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. (
  • Mitochondrial ribosomes are a patchwork of core proteins that share homology with prokaryotic ribosomal proteins and mitochondria-specific proteins, which can be unique to different organisms. (
  • The mitoribosome consists of proteins that share homology with bacterial ribosomes, some of which can have mitochondria-specific extensions, and additional, mitochondria-specific proteins that decorate the ribosomal surface, the mRNA entrance site and form some of the bridges linking the small and large subunits [ 6 , 7 , 9 , 10 ]. (
  • ClusPro was used to dock this structure prediction to a homology model of E. coli FtsZ resulting in a favourable predicted interaction mode. (
  • We derived cytotoxic T-cell, T-Helper, B-cell and IFN-γ targeting epitopes from surface glycoprotein G. Cytotoxic T-cell specific epitopes, HLA-B*4402, chimeric multiepitope vaccine structures were prepared using homology modelling method. (
  • b Tertiary structure of a section of GlSec61α obtained by homology modeling based on 2WWB ( i , ii and iii ) and 3J7Q ( iv , v and vi ). (
  • Each of the homology modeled structures underwent molecular dynamic simulation for 30 ns, with ( iii and vi ) or without ( ii and v ) docked RNA. (
  • Considering the functional importance and lack of X-ray crystal structure of ABCC5, present work was undertaken to construct 3D structure of protein using homology modeling protocol of YASARA structure (V. 16.3.28). (
  • In this study, multiple homology models of ABCC5 are constructed on the X-ray crystal structure of five different ABC transporters (PDB IDs: 4F4C, 4Q9H, 4M1M, 4M2T and 4KSD) and all models are ranked as per their structural quality. (
  • The best homology model of ABCC5 was model number 22 ( Table 1 lists all models that were built on different templates) and this model was based on crystal structure of P-glycoprotein (PDB ID: 4Q9H) of 3.4 Å ( Figure 2 ). (
  • The overall homology based on two separate matrix scoring systems (minimum base change per codon and amino acid homology per residue) is significant. (
  • The recent solution of the crystallographic structure confirms the elements of this homology model. (
  • Secondary structure information and position-specific scoring matrices (PSSMs) are utilized as input features. (
  • They used position-specific scoring matrices (PSSMs) and secondary structure information as features in their prediction model. (
  • The prediction within coil is done by using propensities weighted by scores coming from position specific scoring matrices (PSSMs) generated by PSI-BLAST (Altschul & al. (
  • for each tetrapeptide, a score is evaluated using propensities and PSSMs. (
  • Both PTMs usually occur on disordered regions of protein structure, within which, the location of O -GlcNAcylation and phosphorylation is virtually random with respect to each other, suggesting that negative crosstalk at the structural level is not a common phenomenon. (
  • Benkert, P., Schwede, T., Tosatto, S.C.E. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. (
  • Our in silico structural analysis shows that XLG3 aligns closely to the crystal structure of GPA1, and XLG3 also competes with GPA1 for Gβγ binding in yeast. (
  • We developed a server that integrates predictions of several related descriptors including structural class (17), fold type (23), and secondary structure content (9). (
  • The user can either perform single prediction task, i.e., secondary structure content prediction with PSSC-core (9), structural class prediction with SCEC (17), and fold type prediction with PFRES (23), or (s)he can use the integrated iFC2 server (by pressing on the 'all methods' button), which predicts the three targets at the same time. (
  • For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure. (
  • Secondary structures, because they allow a simple and intuitive description of 3D structures, are widely employed in a number of structural biology applications. (
  • The nucleoprotein (N) is responsible for viral replication and genome wrapping, Matrix protein (M) for structural arrangement and release, Large polymerase (L), Phosphoprotein (P) along with non-structural accessory proteins namely V-protein, C-protein and W-protein play an important role in suppressing α/β interferon (IFN-α/β) production thereby evading innate immune response 10,11 . (
  • Our findings suggest that specific Lysines may be selected for ubiquitination based upon an embedded code defined by a specific amino acid motif with structural determinants. (
  • Furthermore, structure-based virtual screening was carried out against the predicted active site of the respective protein using the glycerol structural analogs from the PubChem database. (
  • In addition, structural features such as secondary structures, surface accessibilities and disorder regions were annotated for the predicted p-sites. (
  • Data from phylogenetic and population genetic analysis of 3,746 gene alignments consistently shows a significantly higher degree of positive Darwinian selection in intrinsically disordered regions of proteins compared to regions of alpha helix, beta sheet or tertiary structure. (
  • These position specific scoring matrices are based on alignments. (
  • In 1951, Pauling and Corey predicted the existence of two periodic motifs in protein structures: the α -helix [ 1 ] and the β -sheet [ 2 ] which turned out to be major features of protein architecture. (
  • The database provides community access to over 400 recognition motifs and position weight matrices for over 200 TFs, including many unpublished motifs. (
  • Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. (
  • We used the PCPMer program to define areas conserved in physical chemical properties (PCP-motifs) of DV proteins of known structure. (
  • Nevertheless, motifs need not be associated with a distinctive secondary structure. (
  • Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell, or mark them for phosphorylation. (
  • To demonstrate the application of the theory, we prove, for the first time, a number of results showing local linear convergence of nonconvex cyclic projections for inconsistent (and consistent) feasibility problems, local linear convergence of the forward-backward algorithm for structured optimization without convexity, strong or otherwise, and local linear convergence of the Douglas-Rachford algorithm for structured nonconvex minimization. (
  • In 2004, we developed a novel algorithm of group-based phosphorylation site predicting and scoring ( GPS ) 1.0 , based on a hypothesis of short similar peptides exhibiting similar biological functions. (
  • GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection. (
  • That is, α helices ( H ), β strands ( E ), and other structures ("coils") defined by DSSP were encoded as H , E , and C , respectively. (
  • The increased ribosomal protein content does not entirely compensate for the loss of rRNA as many of the mitochondria-specific ribosomal proteins do not replace the missing RNA helices but instead have unique positions on the exterior of the mitochondrial ribosome [ 11 , 12 ]. (
  • The secondary structure elements have been marked below the alignment, with spirals representing α-helices, arrows representing β-strands and lines representing intervening loops. (
  • Proteins in this family share similar predicted secondary structures consisting almost exclusively of α-helices in a probable coiled-coil formation. (
  • The putative structure of ABCC5 consists of 12 transmembrane helices (TMH) and 2 NBDs ( Figure 1 ). (
  • 2000). Cytogenetically INPP5E is positioned on 9q34.3 locus. (
  • Aleshin AE, Kirby Ch, Liu X, Bourenkov GP, Bartunik HD, Fromm HJ, Honzatko RB (2000) Crystal structures of mutant monomeric hexokinase I reveal multiple adp binding sites and conformational changes relevant to allosteric regulation. (
  • Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. (
  • Kountouris, P., Hirst, J.D.: Prediction of backbone dihedral angles and protein secondary structure using support vector machines. (
  • Protein secondary structure refers to the local conformation proteins' polypeptide backbone. (
  • Our results suggest that enormous diversity of vertebrate multiple variable first exons is achieved through birth-and-death evolution and that adaptive evolution of specific codon sites enhances vertebrate UGT diversity for defense against environmental agents. (
  • We implemented a program CRNPRED which predicts secondary structures, contact numbers and residue-wise contact orders. (
  • CRNPRED achieves, on average per chain, Q 3 = 81% for secondary structure prediction, and correlation coefficients of 0.75 and 0.61 for contact number and residue-wise contact order predictions, respectively. (
  • One-dimensional (1D) structures of a protein are residue-wise quantities or symbols onto which some features of the native three-dimensional (3D) structure are projected. (
  • Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. (
  • Protein inter-residue contact prediction is one of the problems being actively studied in the structure prediction community. (
  • The patterns are expressed as a set of high-dimensional state vectors which are used as input variables for a simple linear regression to produce predicted secondary structures, contact numbers and residue-wise contact orders. (
  • The several properties of it, including its pH and temperature optima, the high affinity to substrates and high specific activity, make it has great potential to be utilized as supplementation in conversion of corncob residue and other lignocellulosic biomass into simple sugars. (
  • For constructing a simple frequency matrix, a residue substitution matrix, gap opening and gap extension penalty must be specified. (
  • Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. (
  • The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure. (
  • For ß turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED. (
  • The basic principle is to predict first secondary structures with an accurate method such as PSIPRED (Jones, 1999), and to predict beta-turns within (almost) coil regions. (
  • Secondary structure prediction, using Psipred . (
  • Secondary structure elements were independently predicted using PSIPRED v2.5 [ 12 ] and the prediction was overlaid on the three-dimensional model with color-coding corresponding to the type of elements. (
  • Comparative analyses and homologous modeling demonstrated that vertebrate UGT proteins have similar three-dimensional structures each with N-terminal and C-terminal Rossmann-fold domains binding acceptor and donor substrates, respectively. (
  • We can say that in nature the primary structure determines the secondary structure and the secondary structure decides the tertiary structure and then the quaternary structure. (
  • Accurate prediction of intrinsically disordered proteins and regions is critical for both basic research (such as protein structure and function prediction) and practical applications (such as drug development). (
  • intrinsically disordered proteins and regions, physicochemical-based method, machine-learning-based method, template-based method, meta method Introduction Proteins and protein regions without a stable three-dimensional structure are called intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) [1, 2]. (
  • We also considered their secondary structure and distinguished between helix (H), sheet (E) and loop (C). We also took two different substitution matrices into account, BLOSUM62 and PAM250. (
  • Various reports related to SARS-CoV-2 suggest a correlation between neutralizing antibodies and the number of specific T cells to viral particles ( 8 ). (
  • Sazanov, L. A. A giant molecular proton pump: structure and mechanism of respiratory complex I. (
  • We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. (
  • However, its three-dimensional structure is unavailable and the molecular basis of its permeation function is unknown. (
  • 2] M. J. Berardi, W. M. Shih, S. C. Harrison, and J. J. Chou, "Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching," Nature No.476, pp. 109-113, 2011. (
  • Here, we use quantitative molecular-modeling methods to derive a structure of the a - c complex that is not only objectively consistent with the cryo-EM data, but also with correlated mutation analyses of both subunits and with prior cross-linking and cysteine accessibility measurements. (
  • Learning systems have a long history in being applied to reduce the search space for protein structure prediction e.g. artificial neural networks (ANN) and hidden markov models (HMM) are used for protein secondary structure prediction and motif recognition. (
  • PREDICTING PROTEIN SECONDARY STRUCTURE USING ARTIFICIAL NEURAL NETWORKS, - Title: PowerPoint Presentation Author: Valued Sony Customer Last modified by: njit Created Date: 4/29/2002 1:34:55 AM Document presentation format, Towards Efficient Learning of Neural Network Ensembles from Arbitrarily Large Datasets. (
  • Conformation generation of protein-bound peptides is critical for the determination of protein-peptide complex structures. (
  • Recently, we released GPS 5.0 , by developing two novel methods of position weight determination ( PWD ) and scoring matrix optimization ( SMO ) to improve the performance for predicting kinase-specific p-sites. (
  • Analyses of selection yielded one housekeeping gene and 7 virulence genes which showed significant evidence of positive selection at loci implicated in cell surface structures and membrane proteins, metabolism and biosynthesis, transcription, translation and cell separation, and substrate binding and transport. (
  • A structure similarity-based network was used to identify a U-shaped helix-turn-helix candidate fold as being favoured. (
  • The interaction of CENP-N with CENP-A and the nucleosomal DNA together ensure specific and stable centromeric nucleosome recognition. (
  • Structure Classification-based assessment of CASP3 predictions for the fold recognition targets. (
  • this list allows the user to choose a secondary structure prediction method used with COUDES (by default, COUDES predicts beta-turns only within coil regions). (
  • How CRNPRED predicts 1D structures? (
  • Most of the state-of-the-art methods for protein seconday structure prediction are complex combinations of discriminant models. (
  • The most reliable methods for identification of protein structure are X-ray crystallography techniques, but they are expensive and time-consuming. (
  • A number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. (
  • In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. (
  • In recent years, secondary structures have come to play a major role in a number of methods aiming at predicting protein 3D-structures. (
  • The structures were validated using various methods and docking simulation was performed between epitopes and HLA-B*4402. (
  • Deriving stable microarray cancer-differentiating signatures by machine learning and feature-elimination methods, and evaluating consensus scoring of multiple random sampling and Gene-Ranking's consistency. (
  • Later, we presented GPS 2.0 and 2.1 (renamed as Group-based Prediction System), in which two methods of matrix mutation (MaM) and motif length selection (MLS) were designed to improve the prediction accuracy, whereas the scoring strategy of GPS 1.0 & 1.1 was not changed. (
  • CRNPRED will be a useful tool for computational as well as experimental biologists who need accurate one-dimensional protein structure predictions. (
  • Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. (
  • 1] J. R. Schnell and J. J. Chou, "Structure and mechanism of the M2 proton channel of influenza A virus," Nature No.451, pp. 591-595, 2008. (
  • Importantly, the knowledge of protein structures is a foundation for understanding the mechanism of diseases of living organisms and facilitating discovery of new drugs. (
  • In this study, we focused on the mechanism by which TRAF6, along with p62, targets specific Lysines for ubiquitination. (
  • Crystal structure and mechanism of a calcium-gated potassium channel. (
  • Ye, S., Li, Y., Chen, L. & Jiang, Y. Crystal structures of a ligand-free MthK gating ring: insights into the ligand gating mechanism of K + channels. (
  • Background: Immune reaction is the most important defense mechanism for destroying invading pathogens in our body, and the epitope is the position of the antigen-antibody interaction on pathogenic proteins. (
  • However, insufficient information on the structure of the a - c complex has hindered a more detailed understanding of this unparalleled energy conversion mechanism. (
  • For example, MELD can be directed to "make a good hydrophobic core" or "make secondary structures consistent with Web server predictions" ( 5 ). (
  • 3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach. (
  • These predictions drive de novo prediction of protein tertiary structure towards better results by reducing the conformational space. (
  • The cross-evaluation results include the secondary structure contents of helix and strand re-predicted by iFC2 server (which is potentially different from the predictions of PSSC-core (9)), the output label provided by iFC2 server which flags the prediction of SCEC as potentially correct or incorrect, and the label generated by iFC2 server that annotates the prediction of PFRES as potentially correct or incorrect. (
  • Ginalski K, Elofsson A, Fischer D, Rychlewski L (2003) 3D-Jury: a simple approach to improve protein structure predictions. (
  • CPS production is driven mostly by the expression of genes located in a locus called cps , and the resulting structure is used to distinguish between different serotypes (K types). (
  • On average, MODPEP obtained a success rate of 74.3% for all the 910 peptides and ≥ 90% for short peptides with 3-10 amino acids in reproducing experimental protein-bound structures. (
  • We have used genome-wide strain-specific single nucleotide polymorphism data from 64 strains of budding yeast ( Saccharomyces cerevisiae or Saccharomyces paradoxus ) to determine whether adaptive positive selection is correlated with protein regions showing propensity for different classes of structure conformation. (
  • Periostin (POSTN) is a secreted extracellular matrix protein of poorly defined function that has been related to bone and heart development as well as to cancer. (
  • A β -turn is a secondary protein structure type that plays a significant role in protein configuration and function. (
  • Thus computational tools for predicting protein structure and function are highly needed to narrow the widening gap [ 3 ]. (
  • Scoring function for automated assessment of protein structure template quality. (
  • is a major advance toward understanding structure-function relationships in this important class of transporters. (
  • The output of the ANN can be translated into a potential and used as additional component in the scoring function fro de novo protein structure prediction. (
  • Perhaps this conserved secondary structure accounts for the role of the non-conserved interdomain loop in TetA function. (
  • The biological function of a short peptide is related to its three-dimensional structure within its interacting protein. (
  • It is crucial for understanding protein structure and function. (
  • They provide an important alternative for analysis/prediction of the protein structure/function. (
  • Together, these results indicate an essential function for the predicted βCOP appendage and suggest that both COPI appendages perform a biologically active regulatory role with a structure related to adaptin-family appendage domains. (
  • The mechanistic understanding of potential cold tolerance induced by the protein however remains obscure due to lack of knowledge about its structure and precise biological function. (
  • Unfortunately, researchers pay more attention to the structure and function of different secretion systems, rather than their secretory products [7]. (
  • However, the capacity for directed enzyme design requires an understanding of CESA protein structure/function relationships. (
  • A protein's function can be determined by its structure. (
  • Testis-specific YRV is abolished in genotypes with heterozygous loss-of-function mutations for mod(mdg4) and Su(var)205 but not in similar experiments with JIL-1. (
  • Artificial Neural Network (ANNs) are programs designed to solve any problem by trying to mimic the structure and the function of our nervous system. (
  • In comparative modeling, protein structures are inferred from a database of other already-known protein structures. (
  • Evaluation of comparative protein structure modeling by MODELLER 3. (
  • Qian, N., Sejnowski, T.J.: Predicting the secondary structure of globular proteins using neural network models. (
  • Two systems assembled fragments produced by a generative neural network, one using scores from a network trained to regress GDT_TS. (
  • One such problem, which is one of the fundamental open problems in computational biology is the prediction of the 3D structure of proteins, or protein structure prediction (PSP). (
  • Computational results support the importance of the plant-conserved region and/or class-specific region in CESA oligomerization to form the multimeric cellulose-synthesis complexes that are characteristic of plants. (
  • The process of signal transduction is dependent upon specific protein-protein interactions, with a small number of proteins - called 'hubs' possessing the ability to interact with many different partners to form multimeric signaling complexes referred to as signalsomes. (
  • Messenger RNAs encoded by mitochondrial genomes are translated on mitochondrial ribosomes that have unique structure and protein composition. (
  • Method: First, we built five SVM models in the first layer according to five features, including binary composition, position-specific scoring matrix, secondary structure, accessible surface area, and association rule, and then chose the patterns that exhibited the best performance in each model. (
  • Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures). (
  • A large number of servers and tools are used to predict the secondary structure analysis. (
  • Therefore, accurate prediction of 1D protein structures is of fundamental biological interest. (
  • Successful protein structure identification enables researchers to estimate the biological functions of proteins, yet it remains a challenging problem. (
  • Self-interactions Proteins (SIPs) is important for their biological activity owing to the inherent interaction amongst their secondary structures or domains. (
  • Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. (
  • It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition. (
  • A key test of any method for predicting protein structures is CASP (Critical Assessment of Structure Prediction), a blind assessment event of a community involving close to 200 research groups ( 3 ). (
  • These data, together with the significant performance of automated I-TASSER server (the Zhang-Server) in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP)7 experiment, demonstrate new progresses in automated ab initio model generation. (
  • The performance of 40 state-of-the-art predictors is directly compared on the target proteins in the task of disordered region prediction in the 10th Critical Assessment of protein Structure Prediction. (
  • Here we show that a point mutation in a mammalian-specific ribosomal protein causes mitochondrial dysfunction, heart abnormalities and progressive liver disease. (
  • Importantly, further strong support derived from a previously characterised insertion mutation, known to abolish GP0.4 activity, that is positioned in close proximity to the proposed GP0.4/FtsZ interface. (
  • While a score of 0 shows that the substitution occurs randomly, a negative one points to a mutation less frequent than a random mutation. (
  • Mutation of serine (blue) to arginine (orange) on position 77. (
  • Mutation of leucine (blue) to phenylalanine (orange) on position 213. (
  • Mutation of glycine (blue) to glutamic acid (orange) on position 241. (
  • Mutation of valine (blue) to isoleucine (orange) on position 349. (
  • Mutation of threonine (blue) to methionine (orange) on position 408. (
  • Continuous mutation at positions that are non-essential for replication allows flaviviruses to evade or confuse the immune system. (