• Secondary structure can be predicted from one or several nucleic acid sequences. (wikipedia.org)
  • A proportion of these will alter protein sequences, the most common of which is the non-synonymous single nucleotide polymorphism (nsSNP). (biomedcentral.com)
  • ranking at the proportional linear human rape strategies embedded in this continuity, we have that the structure is Lax-Milgram UsePrivacy and the distinct failure of Sobolev sequences and its functions. (aeogroup.net)
  • alignment - A comparison of two or more gene or protein sequences in order to determine their degree of similarity in amino acid or bases, respectively. (rcsb.org)
  • Fig. 1: Photochemistry of light-oxygen-voltage receptors and sequences of proteins under study. (nature.com)
  • Using a homology search, we obtained a set of candidate sequences, modelled the tertiary structure of the selected enzymes, and compared them with experimental and model structures of known DAAOs. (actanaturae.ru)
  • Standard protein chemistry techniques were applied to sequence all the fragment peptides from a tryptic digest of c 550 . (caltech.edu)
  • This information was combined with a 2.45 Å electron density map of the protein where identifying the tryptic fragments in the map led to the correct ordering of the peptides and the final complete sequence. (caltech.edu)
  • Bioinformatic algorithms allowing predicting of biomolecular folding for proteins, peptides, and RNAs, even though sometimes successful, have all their limitations. (biosyn.com)
  • RNA molecules in solution may adopt secondary structures that are only partially determined by thermodynamics since RNA molecules can undergo conformational changes during interaction with other RNAs, RNA binding proteins or RNA binding peptides. (biosyn.com)
  • This paper describes results on the association between protein kinase A and peptides corresponding to wild-type PLN (residues 8-22) and peptides bearing mutations (R9C and A11E) which in the context of full-length PLN (52 residues) result in dilated cardiomyopathy. (elifesciences.org)
  • There are 20 different alpha amino acids commonly found in nature that can covalently link with each other to form short peptides or longer proteins. (rcsb.org)
  • Nevertheless, even the conformational heterogeneity of globular proteins due to their internal dynamics requires the use of such representations. (biomedcentral.com)
  • A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand �-sheet holding two �-helices of three and four turns that are oriented antiparallel to the �-strands. (pdfroom.com)
  • This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold. (pdfroom.com)
  • Resonance Group, Chemical of the globular proteins bovine pancreatic trypsin inhibitor (BPTI) and Center, Lund University ubiquitin in aqueous solution. (lu.se)
  • This difference was ascribed to the abscence, in ubiquitin, of highly ordered internal water molecules, which are known to be present in BPTI and in most other globular proteins. (lu.se)
  • It is believed that the systematic approach outlined in this study may be used as a template to unravel the structure-function relationships of many other biologically important enzymes. (iucr.org)
  • Currently, there are no structural studies of any of its enzymes, hence the determination of the three-dimensional (3D) structure of Pi GlcK-1 becomes a significant contribution to the deduction of its functions, its interaction with ligands, and possible regulatory mechanisms. (scientificarchives.com)
  • A structural comparison of the predicted model with other structures of crystallized glucokinases enzymes allowed us to identify both the regions of interaction with their classical substrates (glucose and ATP) and those involved in the binding of other substrates such as fructose and ADP. (scientificarchives.com)
  • The high variability in the primary structures of DAAO severely limits the search for new enzymes in known genomes. (actanaturae.ru)
  • The protein sequence and the three-dimensional folding structure for cytochrome c 550 from Micrococcus denitrificans are reported. (caltech.edu)
  • The structural comparison of binding sites is especially useful when applied on distantly related proteins as a comparison solely based on the amino acid sequence is not sufficient in such cases. (uni-marburg.de)
  • BipD is similar in sequence to IpaD from Shigella and SipD from Salmonella and is therefore likely to be a translocator protein in the type-III secretion system of B. pseudomallei. (rcsb.org)
  • Nucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. (wikipedia.org)
  • Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known). (wikipedia.org)
  • many molecules have several possible three-dimensional structures, so predicting these structures remains out of reach unless obvious sequence and functional similarity to a known class of nucleic acid molecules, such as transfer RNA (tRNA) or microRNA (miRNA), is observed. (wikipedia.org)
  • A common problem for researchers working with RNA is to determine the three-dimensional structure of the molecule given only a nucleic acid sequence. (wikipedia.org)
  • [6] For longer molecules, the number of possible secondary structures is huge: a sequence of 100 nucleotides has more than 10 25 possible secondary structures. (wikipedia.org)
  • Assessment is concentrated on the long-range contacts (separation of the interacting residues of at least 24 positions along the sequence) as these are the most valuable for structure prediction. (predictioncenter.org)
  • Analysis of the Effects of Multiple Sequence Alignments in Protein Secondary Structure Prediction. (auth.gr)
  • Searching for Representations to Improve Protein Sequence Fold-Class Prediction. (auth.gr)
  • MitoProteome: mitochondrial protein sequence database and annotation system. (auth.gr)
  • In the present report we have compared and contrasted structure- and sequence-based methods of prediction to over 5500 genes carrying nearly 24,000 nsSNPs, by employing an automatic comparative modelling procedure to build models for the genes. (biomedcentral.com)
  • For over 40% of the nsSNPs, structure-based methods predicted which of these sequence changes are likely to either disrupt the structure of the protein or interfere with the function or interactions of the protein. (biomedcentral.com)
  • The most identifiable category of SNP is the small proportion (less than 1%) that change protein sequence, the most common of which is the non-synonymous SNP. (biomedcentral.com)
  • We are Critical to answer the synteny developed with misconfigured standing male structure customs and fit it in the importance that we can only Learn through the sequence properties did. (aeogroup.net)
  • In addition to angles, we make use of sequence properties like secondary structure at each time-step, without using any database. (sciencegate.app)
  • Abietane-Type Diterpenoids Inhibit Protein Tyrosine Phosphatases by Stabilizing an Inactive Enzyme Conformation. (colorado.edu)
  • Our structures, combined with the results from other biophysical and biochemical assays, reveal a common disease mechanism: the mutations in PLN reduce its phosphorylation level by changing its conformation and weakening its interactions with PKA. (elifesciences.org)
  • After obtaining his degree in 1997, he worked as a Wellcome Trust and BBSRC Research Fellow, designing joint theoretical and experimental approaches to study the dynamic conformation of hyaluronan, both free and in the presence of protein, and expanding his research into other polysaccharides and oligosaccharides. (gr.jp)
  • 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)
  • In general, most genes that encode antigens of Plasmodium parasites are highly polymorphic and encode proteins that are important targets for host protective antibody responses [ 5 ]. (biomedcentral.com)
  • Computational protein structure prediction remains one of the most challenging problems in structural bioinformatics. (biomedcentral.com)
  • 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)
  • Conversely, bioinformatics tools offer an alternative that allows prediction of 3D protein structures by molecular dynamics and homology modeling making it faster, cheaper, and highly reliable. (scientificarchives.com)
  • An extensive bioinformatics analysis of the coronavirus replicase proteins by Snijder et al. (pdfroom.com)
  • TARGET: a new method for predicting protein subcellular localization in eukaryotes. (auth.gr)
  • Most folding algorithms use approximations for scanning the landscape of possible secondary structures. (biosyn.com)
  • In addition to their occurrences in several double stranded stem regions, most of the loops and bulges that appear in single-stranded RNA secondary structures form recurrent 3D motifs, where non-canonical base pairs play a central role. (wikiversity.org)
  • This article is about the computational prediction of nucleic acid structure. (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)
  • Mechanistically, QL-007 blocked the encapsidation of pgRNA and induced aberrant polymers assembly at concentrations ≥100 nM, while having no impact on the stability of core proteins. (bvsalud.org)
  • Summing the free energy for such interactions should provide an approximation for the stability of a given structure. (wikipedia.org)
  • 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)
  • This is the first three-dimensional structure of a glycosylated module of fibronectin, and provides insight into the possible role of the glycosylation in protein stability, protease resistance and modulation of collagen binding. (embl.de)
  • While stability of the monomer of TTR decreases in the presence of Zn(2+), which is consistent with the tertiary structural perturbation provoked by Zn(2+) binding, tetramer stability is only marginally affected by Zn(2+). (rcsb.org)
  • For experimental methods, see Nucleic acid structure determination . (wikipedia.org)
  • active site - A region in proteins and nucleic acids (that participate in chemical reactions), where reacting molecules (substrates) bind and make specific contacts necessary for chemical catalysis. (rcsb.org)
  • Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. (pdfroom.com)
  • The mapping of RNA-protein or RNA-RNA interactions by protein pull-down or affinity pull-down methods allow studying RNA structures, as well as RNA-protein, and RNA-RNA interactions. (biosyn.com)
  • By employing this information, molecule libraries can be filtered for subsequent affinity assays and molecular structures can be refined with regard to affinity and selectivity. (uni-marburg.de)
  • 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)
  • Aptamers are single-stranded RNA or DNA oligonucleotides that fold up into a distinctive 3D structure capable of binding with high affinity and specificity to small molecules up to entire organisms, with nanomolar range dissociation constants. (encyclopedia.pub)
  • TTR affinity for holo-RBP decreases ∼5-fold in the presence of Zn(2+). (rcsb.org)
  • Determining high-resolution structures of biological macromolecules amassing less than 100 kilodaltons (kDa) has been a longstanding goal of the cryo-electron microscopy (cryo-EM) community. (nature.com)
  • Orthologues identified by transcriptome sequencing were characterized using phylogenetic, ab initio protein modelling and comparative and population-based methods. (biomedcentral.com)
  • The tertiary structure resulted from an x-ray crystallographic determination. (caltech.edu)
  • This resolution regime has also expanded the potential of cryo-EM SPA for structure-based drug design, particularly for targets that are less amenable to other structure determination techniques due to limited sample quantity or recalcitrance to crystallization. (nature.com)
  • Despite these advances, the radiation sensitivity of ice-embedded proteins and the low signal-to-noise ratio (SNR) of cryo-EM images nonetheless impede routine structure determination for all samples, and specimen size remains a considerable limiting factor in cryo-EM SPA. (nature.com)
  • However, experimental determination of protein structures remains a costly and time-consuming challenge. (scientificarchives.com)
  • Our results present a new conceptual method for the evaluation of dynamic conformational ensembles resulting from NMR structure determination. (biomedcentral.com)
  • Accuracy can only be reliably assessed by means of independent measurements which can range from obtaining distinct parameter sets not used for structure calculations (cross-validation) to the reproduction of the full structure determination procedure by a different research group. (biomedcentral.com)
  • Structure, Function and Dynamics of Lipid Bilayers K. M. Merz, Jr. (wikipedia.org)
  • How the NC dynamics at the exit tunnel affect NC folding remains to be an important question, the answer on which has strong implications to medicine. (biorxiv.org)
  • In conjunction with the recognition of the functional role of internal dynamics of proteins at various timescales, there is an emerging use of dynamic structural ensembles instead of individual conformers. (biomedcentral.com)
  • For both proteins, the oxygen-17 relaxation depended only very weakly on pD, showing that ionic residues do not perturb hydration water dynamics more than other surface residues. (lu.se)
  • Over the last decades, a variety of RNA methods have been developed for the study of RNA-DNA, RNA-RNA, and RNA-protein interactions including RNA complexes with ligand molecules. (biosyn.com)
  • RNA molecules are functionally diverse and involved in many cellular processes such as catalysis, ligand binding, and protein recognition. (biosyn.com)
  • In the present work, accelerated methods for the comparison of protein binding sites as well as an extended procedure for the assessment of ligand poses in protein binding sites are presented. (uni-marburg.de)
  • Methods for the assessment of ligand poses in protein binding sites are also used in the early phase of drug development within docking programs. (uni-marburg.de)
  • How to Measure the Similarity Between Protein Ligand-binding Sites. (uni-marburg.de)
  • The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria. (uni-marburg.de)
  • This binding occurs at a site different from the proteins active site and enhances or reduces the protein's reactivity towards its normal ligand. (rcsb.org)
  • The tertiary structure of the glycosylated second type 2 module (2F2) from the gelatin-binding domain of fibronectin was determined by two-dimensional nuclear magnetic resonance spectroscopy and simulated annealing. (embl.de)
  • AbstractComputational methods that produce accurate protein structure models from limited experimental data, e.g. from nuclear magnetic resonance (NMR) spectroscopy, hold great potential for biomedical research. (sciencegate.app)
  • 2009 Nuclear Magnetic Resonance Structure of the. (pdfroom.com)
  • Template-based modeling, including protein threading and homology modeling, is a popular method for protein tertiary structure prediction. (biomedcentral.com)
  • These results demonstrate that with the help of deep learning, ThreaderAI can significantly improve the accuracy of template-based structure prediction, especially for distant-homology proteins. (biomedcentral.com)
  • The reliability of these tools is based on the use of databases of solved protein structures that can serve as homology templates in the simulation and structural prediction of proteins [ 5 ]. (scientificarchives.com)
  • RNA molecules are structural flexible and can adopt different structures. (biosyn.com)
  • RNA molecules are generally folded into compact and defined tertiary structures. (biosyn.com)
  • The nature of the chemical bond and the structure of molecules and crystals. (uni-marburg.de)
  • Secondary structure of small RNA molecules is largely determined by strong, local interactions such as hydrogen bonds and base stacking . (wikipedia.org)
  • Search Rhea for molecules that contain or resemble this structure. (rhea-db.org)
  • includes analogous molecules, computer-generated graphics, and mechanical structures. (lookformedical.com)
  • The structures of polynucleotide strands of both DNA and RNA molecules can be understood in terms of sugar-phosphate backbones consisting of phosphodiester-linked D 2' deoxyribofuranose (D ribofuranose in RNA) sugar moieties, with purine or pyrimidine nucleobases covalently linked to them. (wikiversity.org)
  • Most of these play very important roles in shaping the structure and function of different functional RNA molecules. (wikiversity.org)
  • These observations demonstrate that the water relaxation dispersion in protein solutions is essentially due to a few structural water molecules buried within the protein matrix, but exchanging rapidly with the external water. (lu.se)
  • The water molecules residing at the surface of the two proteins were found to be highly mobile, with an average rotational correlation time of approximately 20 picoseconds. (lu.se)
  • We believe that the present results resolve the long-standing controversy regarding the mechanism behind the spin relaxation dispersion of water nuclei in protein solutions, thus establishing oxygen-17 relaxation as a powerful tool for studies of structurally and functionally important water molecules in proteins and other biomolecules. (lu.se)
  • 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)
  • Moreover, binding site comparisons are used as an idea generator for bioisosteric replacements of individual functional groups of the newly developed drug and to unravel the function of hitherto orphan proteins. (uni-marburg.de)
  • It would be an advantage if the functional effects of an nsSNP on protein structure and function could be predicted, both for the final identification process of a causal variant in a disease-associated chromosome region, and in further functional analyses of the nsSNP and its disease-associated protein. (biomedcentral.com)
  • Currently, several approaches for protein interaction prediction for non-model species incorporate only small fractions of the entire proteomes and their interactions. (biomedcentral.com)
  • In addition, we trained a machine-learning algorithm (Gradient Boosting) using docking information performed on a curated set of positive and negative protein interaction data. (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)
  • protein interaction has still not emerged. (lu.se)
  • Our ~2.7 Å structure of alcohol dehydrogenase (82 kDa) proves that bound ligands can be resolved with high fidelity to enable investigation of drug-target interactions. (nature.com)
  • In this sense, a better understanding of the three-dimensional (3D) structure of this protein, as well as the spatial description of the possible binding sites to various ligands would contribute to the knowledge of potential targets for the design of inhibitors of the enzymatic activity of Pi GlcK-1. (scientificarchives.com)
  • Aptamers are short single-stranded RNA or DNA oligonucleotides capable of folding into complex 3D structures, enabling them to bind to a large variety of targets ranging from small ions to an entire organism. (encyclopedia.pub)
  • The crystal structure of BipD has been solved at a resolution of 2.1 A revealing the detailed tertiary fold of the molecule. (rcsb.org)
  • The longest helices of the molecule form a four-helix bundle and most of the remaining secondary structure elements (three helices and two three-stranded beta-sheets) are formed by the region linking the last two helices of the four-helix bundle. (rcsb.org)
  • The structure suggests that the biologically active form of the molecule may be a dimer formed by contacts involving the C-terminal alpha-helix, which is the most strongly conserved part of the protein. (rcsb.org)
  • However, in the case of RNA much of the final structure is determined by the secondary structure or intra-molecular base pairing interactions of the molecule. (wikipedia.org)
  • allosteric protein - A protein that changes among two or more structural conformations upon binding to a small molecule called an effector. (rcsb.org)
  • Allostery - This is a type of effect seen in proteins where the binding of a molecule, ion etc. to one location can have an impact of the structure and interactions at another location. (rcsb.org)
  • The most extreme examples of this kind of behavior are provided by intrinsically disordered proteins (IDPs) that adopt a plethora of diverse conformations in their free state but, at least some of them, might become fully or partially well ordered upon partner molecule binding [ 8 , 9 ]. (biomedcentral.com)
  • The main evaluation is carried out on the free modeling (FM) target domains, for which structural templates could not be identified even by a-posteriori structure similarity search. (predictioncenter.org)
  • For the prediction of this model, different algorithms were used to find the best annealing, refinement, and qualitative evaluation of them. (scientificarchives.com)
  • We have chosen different ensembles of three proteins, human ubiquitin, a small protease inhibitor and a disordered subunit of cGMP phosphodiesterase 5/6 for detailed evaluation and demonstration of the capabilities of the CoNSEnsX approach. (biomedcentral.com)
  • Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly. (nih.gov)
  • Protein NMR is the method of choice for determining protein structures at the atomic level in solution. (biomedcentral.com)
  • This bacterial c 550 possesses a structure similar to the known cytochromes from eukaryotic sources and from a photosynthetic bacterium. (caltech.edu)
  • Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. (nih.gov)
  • Since RNA-binding proteins (RBPs) are key players in the post-transcriptional regulation of gene expression precise knowledge of their binding sites is critical for determining their molecular function and for understanding their roles in cell development and disease. (biosyn.com)
  • Knowledge of the three dimensional structure of a gene product is of major assistance in predicting and understanding its function, its role within the cell and its role in disease. (biomedcentral.com)
  • 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)
  • According to its primary structure, the PITG_06016 gene encodes for one of the 7 glucokinases present in Phytophthora infestans Pi GlcK-1, the causal agent of late blight disease. (scientificarchives.com)
  • We propose an approach that uses bioinformatic methods in combination with general 3D structure and active center structure analysis to confirm that the gene found encodes D-amino acid oxidase and to predict the possible type of its substrate specificity. (actanaturae.ru)
  • In this study, we describe the effect of a single amino-acid variation on a prototypical enzyme, human carbonic anhydrase II (CA II), by correlating its high-resolution reaction-intermediate structures with the measured kinetic parameters. (iucr.org)
  • In this work we present the first model obtained by in silico tools of the 3D structure of Pi GlcK-1, and the binding sites to its classical substrates glucose and ATP, to fructose and ADP, and a possible binding site to PPi that is proposed as a promising target for the design of an inhibitor of this enzyme. (scientificarchives.com)
  • Refinement of the model, obtained using phases derived from the structure of the same enzyme from Escherichia coli by molecular replacement, is in progress. (cnr.it)
  • Therefore the predicted structures are often just an estimate or approximation and chemical methods are needed to verify the deduced structures. (biosyn.com)
  • The structure prediction methods can follow a completely theoretical approach, or a hybrid one incorporating experimental data. (wikipedia.org)
  • In vivo , DNA structures are more likely to be duplexes with full complementarity between two strands, while RNA structures are more likely to fold into complex secondary and tertiary structures such as in the ribosome , spliceosome , or transfer RNA . (wikipedia.org)
  • The ribosome-NC contacts within the vestibule define these NC pathways and modulate position of a folded immunoglobulin domain outside the ribosome. (biorxiv.org)
  • RNCs comprising the fifth and sixth domains of ABP-120 filamin protein (referred below as FLN5 and FLN6) have been analysed by NMR spectroscopy in the vicinity of the ribosome 17,18,19. (biorxiv.org)
  • Initial analyses of these RNCs revealed the transition of FLN5 to the folded state occurs when it is bound to the ribosome by a linker of approximately 45 amino acids 2, 20. (biorxiv.org)
  • Structural details on the organisation of FLN5 and FLN6 NC within the ribosome and the effect of the ribosome on the folding of FLN5 remains to be understood that would help to address the question on how the ribosome modulates co-translational protein folding. (biorxiv.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. (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)
  • Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. (biomedcentral.com)
  • The core protein allosteric modulators (CpAMs) have shown great potential as highly effective antiviral drugs against hepatitis B virus (HBV) in preclinical studies and clinical trials. (bvsalud.org)
  • See allosteric protein. (rcsb.org)
  • AMA-1 and RON2 of P. gallinaceum are evolutionarily and structurally conserved, suggesting that these proteins may play essential roles for avian malaria parasites to invade host erythrocytes. (biomedcentral.com)
  • In secondary meta-analyses, the data were grouped across primary categories, and in tertiary analyses, by medication status and absence of psychiatric comorbidity. (psychiatryonline.org)
  • The tertiary analyses (clinical subtypes) showed improved convergence relative to the secondary analyses. (psychiatryonline.org)
  • The work will be of interest to investigators of mechanisms of substrate recruitment by protein kinases, and particularly to those who are trying to understand the mechanisms of familial dilated cardiomyopathy. (elifesciences.org)
  • We generate condensed molecular structures as a refinement-backmapping-of a coarse-grained structure. (tristanbereau.com)
  • Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. (colorado.edu)
  • Predicting pseudoknots and long-range and tertiary-structure interactions accurately is also quite difficult. (biosyn.com)
  • Specific tertiary structure types are observed for transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), certain introns, and ribozymes. (biosyn.com)
  • The perfect addition to any synthetic chemistry laboratory, the XtaLAB mini II single crystal X-ray diffractometer will enhance research productivity by offering affordable structure analysis capability without the necessity of relying on a departmental facility. (rigaku.com)
  • All four structures reveal three tetra-coordinated Zn(2+)-binding sites (ZBS 1-3) per monomer, plus a fourth site (ZBS 4) involving amino acid residues from a symmetry-related tetramer that is not visible in solution by NMR. (rcsb.org)
  • 3-10 helix - A type of protein secondary structural element that is more tightly coiled than the alpha helix (3 amino acids per turn with 10 atoms in the ring completed by each intra-helical hydrogen bond). (rcsb.org)
  • amino acid - A building block of proteins is an alpha amino acid which contains a basic amino group, an acidic carboxyl group, and a hydrogen or organic side chain attached to the central carbon atom. (rcsb.org)
  • These RNC structures reveal a range of pathways adopted by the NC. (biorxiv.org)
  • Efficient Similarity Retrieval for Protein Binding Sites based on Histogram Comparison. (uni-marburg.de)
  • In particular, in terms of alignment accuracy measured with TM-score, ThreaderAI outperforms HHpred, CNFpred, and CEthreader by 56, 13, and 11%, respectively, on template-query pairs at the similarity of fold level from SCOPe data. (biomedcentral.com)
  • It makes possible to elucidate disease mechanisms, to predict protein functions and to select promising targets for drug development. (biomedcentral.com)
  • RocketX is tested on 483 benchmark proteins and 20 FM targets of CASP14. (sciencegate.app)
  • To predict the folding free energy of a given secondary structure, an empirical nearest-neighbor model is used. (wikipedia.org)
  • 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)
  • TBM method predicts the structure of query protein by modifying the structural framework of its homologous protein with known structure in accordance with template-query alignment. (biomedcentral.com)
  • The interpretation and refinement of the derivatives to produce an accurate protein map is discussed. (caltech.edu)
  • The software provides all the tools you need to generate publication quality data that can be used to determine 3D structures from a variety of structure analysis packages. (rigaku.com)
  • n\nIntervention\n\nTwenty-five grams of isoflavone-rich soy protein (91mg of aglycone weight isoflavones: 52mg genistein, 36mg daidzein, 3mg glycitein) ABT-737 in vivo or milk protein-matched placebo provided daily. (peroxidasessignaling.com)
  • Many secondary structure prediction methods rely on variations of dynamic programming and therefore are unable to efficiently identify pseudoknots . (wikipedia.org)
  • The overall structure is appreciably extended and consists of a bundle of antiparallel alpha-helical segments with two small beta-sheet regions. (rcsb.org)
  • The double helical structures of DNA or RNA are generally known to have base pairs between complementary bases, Adenine:Thymine (Adenine:Uracil in RNA) or Guanine:Cytosine. (wikiversity.org)
  • The backbone atoms of the peptide in this region forms a right handed helical structure, hence the name. (rcsb.org)
  • Motivation: The successful application of deep learning has promoted progress in protein model quality assessment. (sciencegate.app)
  • Our knowledge of thermodynamic rules and parameters that govern folding patterns of RNAs are far from being complete. (biosyn.com)
  • MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. (auth.gr)
  • MITOPRED: a web server for the prediction of mitochondrial proteins. (auth.gr)
  • However, the evolution and structure of mitochondrial genomes (mitogenomes) remain unclear in the Rosaceae family. (biomedcentral.com)
  • Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction. (uni-marburg.de)
  • Knowledge Engineering for Protein Structure and Motifs: Design of a Prototype System. (auth.gr)
  • We previously demonstrated that a transmission electron microscope (TEM) operating at 200 keV equipped with a K2 Summit direct electron detector (DED) could be used to resolve a ~150 kDa protein complex to ~2.6 Å using conventional defocus-based SPA methods 12 . (nature.com)
  • While the methods are similar, there are slight differences in the approaches to RNA and DNA structure prediction. (wikipedia.org)
  • Most popular methods for predicting RNA and DNA's secondary structure involve dynamic programming . (wikipedia.org)
  • From its initial isolation, the properties of HA provided a challenge to classical biophysical methods of analysis, which were primarily developed for proteins and required that the properties approached those of perfect Newtonian solutes. (gr.jp)
  • We evaluated our methods both in generating accurate template-query alignment and protein threading. (biomedcentral.com)
  • Experimental results show that ThreaderAI outperforms currently popular template-based modelling methods HHpred, CNFpred, and the latest contact-assisted method CEthreader, especially on the proteins that do not have close homologs with known structures. (biomedcentral.com)
  • Inspired by the success of non-linear models in TBM methods, we would like to study if we can improve TBM methods' model accuracy using more advanced neural network architecture such as deep residual network which has proven very successful in protein residue-residue contacts prediction. (biomedcentral.com)
  • Traditional protein QA methods suffer from searching databases or comparing with other models for making predictions, which usually fail. (sciencegate.app)
  • Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. (nih.gov)
  • A Geometric Algorithm to Find Small but Highly Similar 3D Substructures in Proteins. (uni-marburg.de)
  • Comparative analysis of six genera from the Amygdaloideae and five from the Rosoideae subfamilies of Rosaceae revealed that three protein-coding genes were absent from the mitogenomes of five Rosoideae genera. (biomedcentral.com)