Primary sequence predicts protein structure tertiary. Medical search. Frequent questions

Deletions of 5 to 8 residues within predicted α- helices resulted in the failure of export of the mutant protein from the cell. (tmu.edu.tw)
Each protein has a characteristic number and sequence of amino acid residues. (creative-proteomics.com)
The sequences of amino acid residues in proteins, or their primary structures, cannot be characterized by NMR or other short-range spectroscopic methods, but only by decoding the DNA used in their syntheses or, if available, X-ray analysis of their single crystals. (ncsu.edu)
We set out to analyse the positions of conserved residues within this domain in detail, and relate the conserved residues to the myosin structure. (embl.de)
Conserved residues in the motor domain have been positioned within the framework provided by the recent crystal structures, thus helping to define those residues involved in actin and ATP binding, in hydrolysis and in conformational change. (embl.de)
A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. (asm.org)
Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. (asm.org)
Replacements that favored (Q44R) or impaired (Q44D) the polar interactions predicted between residues Q44 and D32 did not abolish dimer formation of transiently expressed 3A, indicating that these interactions are not critical for 3A dimerization. (asm.org)
Results: Based on the entropy plot, 3 hypervariable regions (HVR) observed along E2 protein located in residues 133-135, 256-260 and 279-281. (mdm2-inhibitors.com)
The fACCD were found 16.18-82.47 kDa proteins having 149-750 amino acid residues. (springeropen.com)

The primary structure of a protein determines how the protein folds into a unique three-dimensional structure secondary, tertiary, and quaternary structures, which in turn determines the biological function of the protein. (creative-proteomics.com)
Just as the primary sequences of proteins determine their secondary, tertiary, and even quaternary structures, and of course their resultant biological functions, it can logically be presumed that the behaviors of synthetic polymers are also principally the result of their complete structural architectures. (ncsu.edu)
As protein tertiary and quaternary structures and their resulting ultimate functions are determined by their primary sequence of amino acids, so too are the behaviors and properties of synthetic polymers critically dependent on their macrostructures. (ncsu.edu)
Here we revisit tau protein aggregation at primary, secondary, tertiary and quaternary structures. (ibecbarcelona.eu)

Very intriguingly, our RTS-based in-depth proteomic analysis enabled us to identify approximately 5000 novel peptides from the ribosome profiling-based short ORFs encoded in the diversified regions on presumed 'non-coding' nucleotide sequences of mRNAs as well as lncRNAs and nonsense mediated decay (NMD) transcripts. (bvsalud.org)
Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. (limswiki.org)
Molecular cloning, nucleotide sequence, and gene expression in liver and brain. (tcdb.org)
3] "Cloning and nucleotide sequencing of transthyretin (prealbumin) cDNA from rat choroid plexus and liver. (tcdb.org)
Mutational genomics and targeted exome capture identify Sr26 and Sr61 as separate single genes that encode unrelated (34.8%) nucleotide binding site leucine rich repeat proteins. (nature.com)
Sequence-dependent coordination of alkali ions to the nucleotide bases in the minor groove of AT-tract B-DNA has recently been inferred from X-ray crystallography, solution NMR and computer simulations. (lu.se)

Which of the four levels of protein organization has a regular repeating structure arising from interactions of nearby amino acids? (lecturio.de)
Protein analyses examine the primary structure (amino acids) as well as the secondary folded structure, more complex tertiary structures, and protein interactions. (jax.org)
Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. (biomedcentral.com)
The predicted interactions were obtained from a meta-approach, applying rigid body docking tests and template-based docking on protein structures predicted by different comparative modeling techniques. (biomedcentral.com)
Using this approach, it was possible to confidently predict 681 protein structures and 6198 protein interactions for L. braziliensis , and 708 protein structures and 7391 protein interactions for L. infantum . (biomedcentral.com)
The present study allowed to demonstrate the importance of integrating different methodologies of interaction prediction to increase the coverage of the protein interaction of the studied protocols, besides it made available protein structures and interactions not previously reported. (biomedcentral.com)
As is shown in Table 1 , these methods mostly employ RNA sequence and structural information to predict protein-RNA interactions. (biomedcentral.com)
Oli [ 16 ] uses k-mer frequency as input feature into an SVM classifier to predict RNA-protein interactions. (biomedcentral.com)
Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies, and the modeling of evolution. (limswiki.org)
During viral infection, the ORF55 protein exerts its biological function through interactions with host proteins. (biomedcentral.com)
A detailed understanding of the molecular biology of parasitic helminths, and in particular of the structure and function of key genes and gene products playing essential roles in host-parasite interactions, could provide a basis for the design of novel therapeutics. (biomedcentral.com)
Compelling evidence for sequence-dependent intrusion of interactions under physiologically relevant solution conditions. (lu.se)

Their alpha-helix and beta-strand sequences have the same proportions of amino acids. (lecturio.de)
Predicting the tertiary (3-dimensional) structure of a folded protein given its primary structure (sequence of amino acids). (gacka.space)
Our results showed that the coding sequence of EZH2 was 2241 bp, encoding 746 amino acids. (hindawi.com)
Consequently, the present situation regarding our ability to characterize the complete chemical structures of synthetic polymers would be analogous to that of proteins if it were only possible to determine their amino acid compositions or possibly the amounts of consecutive pairs or even triplets of constituent amino acids, rather than their complete macrostructures, i.e., their complete amino acid sequences or primary structures. (ncsu.edu)
These sequences tend to be rich in polar amino acids and often escape from the detection of classical bioinformatics screenings that look for highly aggregation-prone hydrophobic sequence stretches. (ibecbarcelona.eu)
Protein are linear chains molecules made up of units called amino acids. (padeepz.net)
Approxoimately twenty different amino acids make up a protein chain. (padeepz.net)
The protein configuration is made primarily by the amino acids side chains. (padeepz.net)
The sequential and linear arrangement of amino acids in a polypeptide represents its primary structure. (padeepz.net)
The computer-generated models depict not only the properties of amino acids in a protein but also help to understand the protein function. (padeepz.net)

Especially, deep learning is increasingly used in the bioinformatics field by virtue of its ability to learn generalized representations from DNA and protein sequences. (biomedcentral.com)
Protein structure prediction is one of the most important scientific problems in the field of bioinformatics and computational biology. (sciencegate.app)
Bioinformatics is the application of computer science and information technology to the field of biology, with a primary goal of understanding biological processes. (limswiki.org)
Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them, and creating and viewing 3-D models of protein structures. (limswiki.org)
Arguably one of the first "bioinformatics" projects-though the concept didn't yet exist-involved the 1965 creation and maintenance of a protein sequence database called the Atlas of Protein Sequence and Structure by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. (limswiki.org)
Bioinformatics is limited to sequence, structural, and functional analysis of genes and genomes and their corresponding products and is often considered computational molecular biology. (limswiki.org)
Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)
As whole genome sequences became available, again with the pioneering work of Frederick Sanger, the term bioinformatics was re-discovered to refer to the creation of databases such as GenBank in 1982. (ind.in)
The primary goal of bioinformatics is to increase the understanding of biological processes. (ind.in)
The study aimed to explore the protein coding ability of the pri-miR156a in Brassicaceae plants using bioinformatics analysis of the available proteomes and translatomes reported for Arabidopsis thaliana. (fortunepublish.com)
Bioinformatics techniques are used to predict B cell and T cell epitopes from the new SARS-CoV-2 spike glycoprotein in order to build a unique multiple epitope vaccine. (springeropen.com)

De novo protein structure prediction methods attempt to predict tertiary structures from sequences based on general principles that govern protein folding energetics and/or statistical tendencies of conformational features that native structures acquire, without the use of explicit templates. (wikipedia.org)
In this chapter, current protein structure prediction methods are reviewed for a milieu on structure prediction, the prediction of structural fundamentals, tertiary structure prediction, and functional imminent. (sciencegate.app)
While developing and evaluating protein structure prediction methods, researchers may want to identify the most similar known structures to their predicted structures. (sciencegate.app)
Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. (biomedcentral.com)

Students will be introduced to biological sequence data (DNA and protein sequences, whole genomes, learn to access major sequence databases and use a variety of web-based services. (uit.no)
The availability of protein three-dimensional (3D) structure is crucial for studying biological and cellular functions of proteins. (sciencegate.app)
Similar to proteins, functional RNA molecules fold into specific three-dimensional conformations essential for performing their biological activity. (biomedcentral.com)
It also includes the study of existing drugs, their biological properties, and their quantitative structure-activity relationships (QSAR). (keywen.com)
2. Protein structures, protein models and computer aided graphic models help to understand biological reactions mediated by enzymes (proteins). (padeepz.net)
Composition & Structure considers the design or control over the components of a material through engineering - either via biological activity or through engineering of the biological component. (ebrc.org)
Composition & Structure considers the design or control over the components of a material through engineering - either via biological activity or through engineering of the biological component - and the two and three dimensional space these components occupy (four-dimensional dynamic activity is found in Properties & Performance ). (ebrc.org)

Their structures cannot be predicted from their primary amino acid sequences. (lecturio.de)
Protein sequencing analysis can directly identify post-translational modifications that cannot be predicted from gene sequences, characterize recombinant proteins, and fragments of natural and recombinant proteins for structural and functional studies. (creative-proteomics.com)

These nucleic acid probes play an important role in cloning new genes encoding low-abundance proteins. (creative-proteomics.com)
For example, genes encoding many important drug proteins used in the clinic. (creative-proteomics.com)
The reports on base sequences of spider silk protein genes have gained importance as the mechanical properties of silk fibers have been revealed. (bioone.org)
Chromatin immunoprecipitation-sequencing profiling demonstrated recruitment of CK2α to active gene loci, more abundantly in late G1 phase than in early G1, notably at transcriptional start sites of core histone genes, growth stimulus-associated genes, and ribosomal RNAs. (bvsalud.org)
In order to further clarify the diagnosis, all the suspected genes in her sister and in their parents were sequenced. (spandidos-publications.com)
The multiplex ligation‑dependent probe amplification project of the Angel/chubby and copy number variation (CNV) sequencing were assessed concomitantly to identify the pathogenic genes responsible for the development of AS. (spandidos-publications.com)
This entailed mining available transcriptomic and/or genomic sequence datasets for the presence of homologues of known TIMPs, predicting secondary structures of defined protein sequences, systematic phylogenetic analyses and assessment of differential expression of genes encoding putative TIMPs in the developmental stages of A. suum , N. americanus and Schistosoma haematobium which infect the mammalian hosts. (biomedcentral.com)
0.001) compared to patients without NI-LGE, with no significant difference in the burden of rare protein altering variants in DCM-associated genes between groups (9.7% vs 6.7%, odds ratio 1.5, 95% CI 0.5-4.4, p=0.41). (imperial.ac.uk)

Protein and peptide interaction prediction and dot-blot overlay assay confirmed that peptides identified by phage display could interact with the ORF55 protein. (biomedcentral.com)
Comparing the peptides to the National Center for Biotechnology Information database revealed four potential interacting proteins. (biomedcentral.com)
PDT allows a direct link and identification between a large number of random peptides and DNA-coding sequences. (biomedcentral.com)

Sequence-structure alignments Sequence-structure alignments were generated and tested both at the sequence level as well as at the 3D level. (keywen.com)
Building upon prior deep learning work utilizing co-evolutionary data from multiple sequence alignments (MSAs) and homologous structures, AlphaFold2 has made remarkable strides in solving this problem for natural proteins with extensive MSAs. (cbirt.net)

A foreign protein is first expressed in fusion with one of the phage capsid proteins by cloning the foreign DNA sequence in frame with the gene encoding the chosen capsid protein [ 22 ]. (biomedcentral.com)
The viral genome encodes four structural capsid proteins (VP1 to VP4) and seven nonstructural (NS) proteins, the leader Lb/ab protease, and proteins encoded in the P2 (2B and 2C) and P3 (3A, 3B, 3C, and 3D) regions ( 9 ). (asm.org)

Sequence and annotate whole genomes of a variety of organisms using the Illumina MiSeq in the Genomics Lab . (rit.edu)
Despite the well-known fact that primiRNAs are acting as non-protein-coding RNAs, the published data suggest that, in the plant genomes, some pri-miRNAs can also be found in polysomes, and the expression of these miRNA precursors may results in formation of micropeptides which may be involved in regulation of gene expression. (fortunepublish.com)

Structure and properties of proteins, nucleic acids, and their complexes. (keywen.com)

Although computational barriers are vast, the potential benefits of structural genomics (by predicted or experimental methods) to fields such as medicine and drug design make de novo structure prediction an active research field. (wikipedia.org)
[3] [4] Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing . (limswiki.org)

At present, some of the most successful methods have a reasonable probability of predicting the folds of small, single-domain proteins within 1.5 angstroms over the entire structure. (wikipedia.org)
Second, DeepSF, a method of applying deep convolutional network to classify protein sequence into one of thousands known folds. (sciencegate.app)
Every protein folds in a particular way to form a distinctive configuration for its specific function. (padeepz.net)
This approach aimed to systematically assess OpenFold's capability to extrapolate to unfamiliar protein folds. (cbirt.net)

Research into de novo structure prediction has been primarily focused into three areas: alternate lower-resolution representations of proteins, accurate energy functions, and efficient sampling methods. (wikipedia.org)

The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. (biomedcentral.com)
A program for homology protein structure modeling by satisfaction of spatial restraints. (keywen.com)
A total of 15 protein sequences with high homology to known eukaryotic TIMPs were predicted from the complement of sequence data available for parasitic helminths and subjected to in-depth bioinformatic analyses. (biomedcentral.com)

Here, we established a Real-Time Search (RTS)-assisted mass spectrometric platform for system-wide quantification of translated products encoded by non-canonical short open reading frames (ORFs) as well as already annotated protein coding sequences (CDSs) on the human transciptome and applied this methodology to quantitative proteomic analyses of suberoylanilide hydroxamic acid (SAHA)-treated human HeLa cells to evaluate proteome-wide regulation in response to drug perturbation. (bvsalud.org)
Inverse-variance weighted MR was utilized for analyses on outcomes of atrial fibrillation, coronary artery disease, heart failure, ischaemic stroke, and 16 measures of cardiac structure and function. (imperial.ac.uk)
Here we show by mass spectrometric analyses of enriched insoluble protein fractions that, unexpectedly, nucleus-encoded transporters are not inserted into the chromatophore inner envelope membrane. (frontiersin.org)
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. (cdc.gov)

However, for a discrete number of patients whose results are uninformative, it may be possible to get a more definitive answer about the consequences of a variant using additional methods like RNA sequencing, protein analysis and predictive or functional studies. (jax.org)
The predicted effects of a variant on functional areas of the protein such as binding sites for DNA or other proteins can also be analyzed. (jax.org)
The proteins take up different profiles as structural and functional proteins such as enzymes and hormones etc. (padeepz.net)

Lee (2020) and Frésard (2019) demonstrated clinical utility in adding RNA sequencing to genomic testing for cohorts of individuals with undiagnosed Mendelian disease, increasing the diagnostic yield by 18% and 7.5%, respectively. (jax.org)
We describe structure-guided engineering of a CRISPR-Cas9 complex to mediate efficient transcriptional activation at endogenous genomic loci. (cdc.gov)

Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. (nature.com)

Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. (nature.com)
Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)

Their work concluded that the overall structural changes between two homologous proteins were proportional to their sequence differences. (biomedcentral.com)
It was then estimated that homologous proteins aligning with less than 20% sequence identity could have large structural differences [ 14 ]. (biomedcentral.com)
In primates (Chimpanzees model in HCV) it's been reported that purified recombinant envelope glycoproteins (E1 and E2) acquired potential to safeguard against problem with homologous trojan, as a result these proteins will be the ideal goals for vaccine advancement (11). (mdm2-inhibitors.com)

The human UBE3A gene encodes an E3 ubiquitin ligase, which exhibits three known protein subtypes ( 1 , 8 ). (spandidos-publications.com)
The viral particle is composed of a protein capsid that contains a positive-sense RNA molecule of about 8,500 nucleotides that is infectious and encodes a single polyprotein, which is processed in infected cells by cis - and trans -acting viral proteases ( 55 ) to yield different polypeptide precursors and the mature viral proteins ( 9 , 62 ). (asm.org)
This RNA includes an open up reading body (ORF) which encodes polyprotein with about 2900 proteins duration. (mdm2-inhibitors.com)
Sr60 is an exception that encodes a tandem kinase protein 10 . (nature.com)

This review aims to link recent molecular data, often translated into amino acid sequences and predicted three dimensional structural motifs, to known mechanical properties. (bioone.org)
This chapter covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. (sciencegate.app)
AbstractProtein structure prediction is a long-standing unsolved problem in molecular biology that has seen renewed interest with the recent success of deep learning with AlphaFold at CASP13. (sciencegate.app)
The macrostructures of synthetic polymers are essentially the complete molecular chain architectures, including the types and amounts of constituent short-range microstructures, such as the regio- and stereosequences of the inserted monomers, the amounts and sequences of monomers found in co-, ter-, and tetra-polymers, branching, inadvertent, and otherwise, etc. (ncsu.edu)
Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. (ind.in)
Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (ind.in)
10] "High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy. (tcdb.org)
Structure is a framework for two-dimensional molecular visualization written in Java and based on Octet. (keywen.com)
HQSAR Hologram QSAR (HQSAR) uses molecular holograms and PLS to generate fragment-based structure-activity relationships. (keywen.com)
SciVision - Databases , molecular modeling , and structure-activity relationship software for Windows. (keywen.com)
Crystal and molecular structure determination. (keywen.com)
The mdxvu program is a molecular dynamics and molecular structure analysis code. (keywen.com)
The Proceedings of this conference have recently been published in the Journal of Molecular Structure (THEOCHEM) vol 368. (keywen.com)
Reverse transcription quantitative PCR results demonstrated high expression of an actin-binding Rho-activating protein in the latter stages of virus-infected cells, and molecular docking, cell transfection and coimmunoprecipitation experiments confirmed that it interacted with the ORF55 protein. (biomedcentral.com)
Conclusions: The extensive analysis of the protein with essential roles hasn't been easy, and in case there is E2 envelope glycoprotein of HGV, there is absolutely no very much data on its immunological and molecular features, clinical significance and its own pathogenic potential in hepatitis or any various other GBV-C related illnesses. (mdm2-inhibitors.com)
A molecular dynamic (MD) modeling approach was applied to evaluate the effect of external electric field on gliadin protein structure and surface properties. (mdpi.com)
In proteomics, to delineate information about a protein at atomic and molecular levels, models are constructed. (padeepz.net)
Engineer metabolic pathways that couple sensing of subtle environmental cues ( e.g., oxygen gradients or mechanical environment) to growth-limiting molecular switches, like lysis proteins. (ebrc.org)

During the course, the students will learn to retrieve, analyze, compare and visualize genetic sequences. (uit.no)
While the genetic DNA code may be read to determine the primary structures of most proteins, we have no such synthetic template for man-made polymers which can be utilized to determine their complete macrostructural architectures. (ncsu.edu)
The work grew out of their "biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code. (limswiki.org)
Angelman syndrome (AS) is an autosomal dominant neurodevelopmental genetic disease with maternal imprint, which is associated with the presence of the abnormal chromosome 15q11‑q13, and the loss of maternal specific expression of ubiquitin‑protein ligase E3A (UBE3A). (spandidos-publications.com)
Among the various genetic metabolic disorders, Angelman syndrome (AS) has attracted considerable attention due to the abnormal expression of the ubiquitin-protein ligase E3A (UBE3A) gene ( 1 ). (spandidos-publications.com)
patients underwent genetic sequencing as part of the research protocol and long-term follow-up. (imperial.ac.uk)
Furthermore, chromatophore-localized biosynthetic pathways as well as multiprotein complexes include proteins of dual genetic origin, suggesting that mechanisms evolved that coordinate gene expression levels between chromatophore and nucleus. (frontiersin.org)
If the results predict CF in the fetus, referral to a tertiary care facility facilitates genetic counseling and consultation with specialists in maternal-fetal medicine. (medscape.com)

For example, whereas X-ray crystallography has been successful in crystallizing approximately 80,000 cytosolic proteins, it has been far less successful in crystallizing membrane proteins - approximately 280. (wikipedia.org)
A total of five major Open Reading Frames (ORF) were found in COVID-19: the ORF 1a/b region coding replicase and other enzymes, the spike or S protein ORF, M or membrane glycoprotein ORF, E or small membrane protein ORF and the N or nucleocapsid ORF ( fig. 1 )[ 5 ]. (ijpsonline.com)
Serine protease present on cell membrane, is used by SARS-CoV-2 for associating spike protein to enable its fusion with host cells[ 12 - 14 ]. (ijpsonline.com)
Based on primary sequence comparisons, β subunits are predicted to be modular structures composed of five domains (A-E) that are related to the large family of membrane-associated guanylate kinase proteins. (jneurosci.org)
in poliovirus (PV), the interaction between the RNA replication complex and intracellular membranes appears to be accomplished by proteins 3A and 2C, which have membrane-binding properties ( 11 , 60 ). (asm.org)
Rational design of synthetic membranes will enable control over the placement and function of membrane components, such as proteins, thus providing an environment for engineering the biotic-abiotic interface when cells and other biomolecules are incorporated. (ebrc.org)
We hypothesize that these proteins are involved in modulating membrane permeability. (frontiersin.org)

Each coil of the helix represents a structural repeat that, in some homologues, can be recognised from sequence information alone. (embl.de)

Another study employed a variational autoencoder to encode AMPs, mapped the probability of being active to a latent space, and predicted novel AMPs [ 9 ]. (biomedcentral.com)
Previously, non-coding RNAs (ncRNAs), including micro-RNAs (miRNAs) and other long non-coding RNAs (lncRNAs), have been generally considered unable to encode proteins both in plants and animals [1-9]. (fortunepublish.com)

Thus proteins fold up in such a way that non-polar-hydrophobic groups remain buried inside the molecule and the polar and charged groups remain outside. (padeepz.net)

RNA testing looks for changes in gene expression, and protein analysis assesses structural changes in the protein product of the gene. (jax.org)
Polycomb Group (PcG) proteins are a family of protein complex that regulate gene expression, especially repressing gene transcription [ 1 ]. (hindawi.com)
Apparently these chromatophore-targeted proteins evolved convergently to plastid-targeted expression regulators and are likely involved in gene expression control in the chromatophore. (frontiersin.org)

There were 9 amino acid insertions and an amino acid substitution in this transcript compared with the validated reference sequence in NCBI. (hindawi.com)
Mammalian NOD1 orthologues were recovered from the NCBI non-redundant protein database using blastp (protein-protein BLAST) with human NOD1 [Genbank: AAD28350.1] as a search term using the standard parameters. (biomedcentral.com)

As one of the two distinct complexes, namely, Polycomb Repressive Complex 1 (PRC1) and PRC2, PRC2 mediates gene silencing by modulating chromatin structure [ 2 ]. (hindawi.com)
Protein signatures associated with nuclear CK2 complexes reveal enrichment of apparently unique transcription factors and chromatin remodelers during progression through the G1 phase of the cell cycle. (bvsalud.org)

abstract = "On the basis of its primary sequence and the location of its disulfide bonds, we propose a structural model of the erythropoietic hormone erythropoietin (Epo) which predicts a four α-helical bundle motif, in common with other cytokines. (tmu.edu.tw)

The distributed representations of RNA sequences and secondary structures can effectively detect the latent relationship and similarity between k-mers, and thus improve the predictive performance. (biomedcentral.com)
These predicted structures often have low sequence and structure similarity to known structures. (sciencegate.app)

The predicted networks were integrated to protein interaction data already available, analyzed using several topological features and used to classify proteins as essential for network stability. (biomedcentral.com)
Rational design of protein structure, activity, and stability. (keywen.com)
The three dimensional shape of a polypeptide is called its tertiary structure.Alpha helices and beta sheets provide further stability to protein structure. (padeepz.net)

Hydrogen bonds between carboxyl groups help stabilize their structures above the primary level. (lecturio.de)
The study of hydrogen bond evolution during the course of simulation revealed that the root mean square deviation, radius of gyration and secondary structure formation, all depend significantly on the number hydrogen bonds formed. (mdpi.com)

However, it is difficult to capture the complexity of transcript isoform variance using these libraries, and large cDNA sequences are often difficult to clone into size-limited viral expression vectors. (cdc.gov)

It was back in the eighties when Chothia and Lesk first quantified such evolutionary relationship for proteins [ 12 - 14 ]. (biomedcentral.com)
The present study unveils the structure-function and evolutionary aspects of 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD) proteins of fungal origin. (springeropen.com)

Tissue inhibitors of metalloproteases (TIMPs) are a multifunctional family of proteins that orchestrate extracellular matrix turnover, tissue remodelling and other cellular processes. (biomedcentral.com)

Comparative evaluation for consensus B-cell epitopes relating to transmembrane topology, predicated on physico-chemical and machine learning strategies uncovered that residue 231- 296 (NH2- EARLVPLILLLLWWWVNQLAVLGLPAVEAAVAGEVFAGPALSWCLGLPVVSMILGLANLVLYFRWL-COOH) is certainly most reliable and possible B cell epitope for E2 proteins. (mdm2-inhibitors.com)

In computational biology, de novo protein structure prediction refers to an algorithmic process by which protein tertiary structure is predicted from its amino acid primary sequence. (wikipedia.org)
De novo methods tend to require vast computational resources, and have thus only been carried out for relatively small proteins. (wikipedia.org)
Prediction of protein structure de novo for larger proteins will require better algorithms and larger computational resources such as those afforded by either powerful supercomputers (such as Blue Gene or MDGRAPE-3) or distributed computing projects (such as Folding@home, Rosetta@home, the Human Proteome Folding Project, or Nutritious Rice for the World). (wikipedia.org)
Based on this perspective, this study presents an integration of computational methodologies, protein network predictions and comparative analysis of the protozoan species Leishmania braziliensis and Leishmania infantum . (biomedcentral.com)
Protein structure prediction and evaluation is one of the major fields of computational biology. (sciencegate.app)

Nuclear expression of protein kinase CK2α is reportedly elevated in human carcinomas, but mechanisms underlying its variable localization in cells are poorly understood. (bvsalud.org)

First, DNSS2, a method for protein secondary structure prediction using one-dimensional deep convolution network. (sciencegate.app)
Protein secondary structure prediction based on position-specific scoring matrices. (keywen.com)

1. Protein structure helps in understanding biomolecular arrangement in tissue or cellular architecture. (padeepz.net)

Several lines of evidence have been presented in favor of the notion that primary protein sequence contains all the information required for overall three-dimensional protein structure, making the idea of a de novo protein prediction possible. (wikipedia.org)
The two dimensional and three dimensional structure of multi-epitope vaccine were predicted and authenticated using PROCheck and Raptor-X servers. (ijpsonline.com)
[2] [5] Six years later, the Brookhaven National Laboratory and the Cambridge Crystallographic Data Centre jointly created the Protein Data Bank, intended as a public database of three-dimensional protein structures. (limswiki.org)
The information regarding three-dimensional structure of protein is stored in another computerized database called Protein Data Bank. (padeepz.net)
Only three dimensional forms are used to define protein structure. (padeepz.net)
Also included is the engineering the physical and bulk characteristics of a material, such as biomolecule ( e.g., protein) structure and three-dimensional architecture of a material. (ebrc.org)

Population conservation studies of the selected protein and predicted epitopes were also performed using population conservancy analysis tool of immune epitope database resource. (ijpsonline.com)

Recombinant protein drugs can also be characterized to ensure that the expressed product conforms to the predicted structure, and to evaluate the quality and purity of the product to be highly consistent. (creative-proteomics.com)
Third, CNNQA and DeepRank, two deep neural network approaches to systematically evaluate the quality of predicted protein structures and select the most accurate model as the final protein structure prediction. (sciencegate.app)

Experimental techniques for determining tertiary structure have faced serious bottlenecks in their ability to determine structures for particular proteins. (wikipedia.org)
In light of experimental limitations, devising efficient computer programs to close the gap between known sequence and structure is believed to be the only feasible option. (wikipedia.org)
Several methodologies, capable of handling and generating large-scale protein interaction data, have been employed, such as the experimental techniques of yeast two-hybrid and affinity purification coupled with mass spectrometry [ 17 ]. (biomedcentral.com)
Our extensive experimental results show that DeepRKE is an efficacious tool for predicting RBP binding sites. (biomedcentral.com)
Similarly, there are currently no experimental means to determine the sequences or locations of constituent microstructures along the chains of synthetic macromolecules. (ncsu.edu)
Intriguingly, heightened performance emerged when training on smaller yet diverse datasets, including those with as few as 1,000 experimental structures. (cbirt.net)

In the last decades, HOX proteins have been extensively studied due to their pivotal role in transcriptional events. (mdpi.com)
For decades, deciphering protein structures from sequences has been a pivotal challenge in biology. (cbirt.net)

Several polypeptide chains form subunits for a large protein. (padeepz.net)

SEquence-structure alignment with 123D+ server. (keywen.com)
The structure of the molecules can be incorporated in the alignment. (keywen.com)
The input to the program was the alignment between the target sequence and template structure(s). (keywen.com)
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints. (keywen.com)

Primary syphilis classically presents as a single painless ulcer or chancre at the site of infection but can also present with multiple, atypical, or painful lesions ( 564 ). (cdc.gov)
Tertiary syphilis can present with cardiac involvement, gummatous lesions, tabes dorsalis, and general paresis. (cdc.gov)
Ocular syphilis often presents as panuveitis but can involve structures in both the anterior and posterior segment of the eye, including conjunctivitis, anterior uveitis, posterior interstitial keratitis, optic neuropathy, and retinal vasculitis. (cdc.gov)
Use of only one type of serologic test (nontreponemal or treponemal) is insufficient for diagnosis and can result in false-negative results among persons tested during primary syphilis and false-positive results among persons without syphilis or previously treated syphilis. (cdc.gov)
Analysis of Treponema pallidum strains from China using improved methods for whole-genome sequencing from primary syphilis chancres. (cdc.gov)

It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. (biomedcentral.com)
The structure of myosin is known, but the actin-binding site is not well defined, and the mechanisms by which actin activates ATP hydrolysis by myosin, and myosin moves relative to the actin filament, developing force, are not fully understood. (embl.de)

An investigation of the methods and algorithms used to predict protein structure and a thorough knowledge of the function and structure of proteins are critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. (sciencegate.app)
All screening algorithms in current use in the United States rely on testing for immunoreactive trypsinogen (IRT) as the primary screen for cystic fibrosis. (medscape.com)

Erythropoietin structure-function relationships. (tmu.edu.tw)
深入研究「Erythropoietin structure-function relationships. (tmu.edu.tw)
For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (ind.in)
Conservation within the myosin motor domain: implications for structure and function. (embl.de)
Structure-function relationships in metalloenzyme mimics. (keywen.com)
E2 envelope proteins of GB trojan Adenosine IC50 C plays function in trojan entry in to the cytosol, genotyping (10), the perfect goals for vaccine advancement, and a marker to diagnose GBV-C attacks (11), and besides, the concomitance between E2 proteins and gp41 proteins of HIV-1 impacts proteins folding and whether it forms a non energetic complicated with gp41-FP. (mdm2-inhibitors.com)
Polymorphisms can affect protein function in unanticipated, and potentially unwelcome, ways. (biomedcentral.com)
Still, the distribution of ACCD in fungal species is limited which consequently limits our understanding of the structure-function aspects of the fungal ACCD (fACCD). (springeropen.com)

Silks are composed principally of proteins with a predominance of alanine, serine and glycine and silk proteins are able to undergo irreversible transformations from soluble protein to insoluble fibres. (bioone.org)

3. Graphic models provided by computers are valuable to predict which fragments of a medically important protein can be used to design drugs and vaccines. (padeepz.net)

CONCLUSIONS: Information from such a sequence analysis is a useful tool in the further interpretation of X-ray structures. (embl.de)

NS proteins are involved in crucial aspects of the viral cycle and pathogenesis, such as rearrangements of intracellular membranes required for endomembrane recruitment and the lysis of host cells ( 1 , 12 , 14 , 18 , 73 ). (asm.org)

GraphProt [ 14 ] adopts the form of graph coding to integrate RNA sequence and structure into the graph kernel to generate a feature vector of more than 3,000 dimensions, which is subsequently used as the input of an SVM model to predict RBP binding preference. (biomedcentral.com)
The proteins are subsequently secreted into the glandular lumen where they are stored until extrusion. (bioone.org)

Anatomy5

Organisms14

Diseases1

Chemicals and Drugs71

Analytical, Diagnostic and Therapeutic Techniques and Equipment59

Phenomena and Processes89

Disciplines and Occupations9

Technology, Industry, Agriculture2

Information Science30

Health Care10

Residues10

Quaternary4

Nucleotide6

Interactions12

Amino acids10

Bioinformatics11

Prediction methods4

Biological7

Cannot be predicted2

Genes8

Peptides3

Alignments2

Capsid proteins2

Genomes2

Nucleic acids1

Genomics2

Folds4

Sampling methods1

Homology3

Analyses4

Functional3

Genomic2

Genome sequences1

Endogenous2

Homologous3

Encodes4

Molecular18

Genetic8

Membrane7

Homologues1

Encode2

Hydrophobic1

Gene expression3

NCBI2

Complexes2

Abstract1

Similarity2

Stability3

Hydrogen2

CDNA1

Evolutionary2

Multifunctional1

Transmembrane1

Computational5

Kinase1

Secondary structure2

Cellular1

Dimensional6

Epitopes1

Evaluate the quality2

Experimental6

Decades2

Subunits1

Alignment4

Syphilis5

Mechanisms2

Algorithms2

Function8

Insoluble1

Fragments1

Conclusions1

Lysis1

Subsequently2