Predictions of solvent accessibility protein structure secondary. Medical search. Frequent questions

Other types of biopolymers such as nucleic acids also possess characteristic secondary structures. (wikipedia.org)
effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. (cicancer.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)

Using a single integrated model, NetSurfP-2.0 predicts solvent accessibility, secondary structure, structural disorder, and backbone dihedral angles for each residue of the input sequences. (ku.dk)
Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. (biomedcentral.com)
For stage one, we trained multiple Support Vector Machines (SVMs) to score eukaryotic protein sequences for membership to each of three categories: nuclear, cytoplasmic and extracellular, plus extra category nucleocytoplasmic, accounting for the fact that a large number of proteins shuttles between those two locations. (biomedcentral.com)
Currently, most protein sequences in databases are the result of translation of hypothetical transcripts derived from genomic sequencing data [ 3 ]. (biomedcentral.com)
Template-based protein modeling techniques exploit the evolutionary relationship between a target protein and templates with known experimental structures, based on the observation that evolutionarily related sequences generally have similar 3D structures. (unibas.ch)
The " Continuous Automated Model EvaluatiOn" (CAMEO) project aims to complement CASP and provide a fully automated blind assessment for prediction servers only based on weekly pre-released sequences of the Protein Data Bank PDB. (unibas.ch)
Misleading signal (or problems with the estimation of significance levels) can be caused by phylogenetic correlations between homologous sequences and from correlation due to factors other than spatial proximity (for example, correlation of sites which are not spatially close but which are involved in common functional properties of the protein). (unimi.it)
In this paper, we propose a new method for protein structural class prediction using low homology (twilight-zone) protein sequences dataset. (bvsalud.org)
Most methods developed for predicting RNA-binding proteins are based on machine-learning methods that employ information of protein sequences and/or known protein structures (5 6 Meanwhile docking techniques for protein-RNA interactions have been developed by using a scoring/energy function for protein-RNA interaction (7-10). (buyresearchchemicalss.net)
Profiles generated using structure-based sequence alignments of distantly related proteins at the family or superfamily level could be utilized to predict the fold of hypothetical sequences through profile-sequence search method is another success in the structure prediction area. (researchsquare.com)
The alignments of protein sequences are required for the organization and assimilation of vast amounts of data. (researchsquare.com)
Multiply aligned set of sequences serve as convenient models to depict evolutionary drifts and provide convenient frameworks for mapping allied information such as secondary structures and functionally important residues. (researchsquare.com)
Genes adjacent to pvtramp were identified in silico to determine the degree of similarity between the protein sequences encoded by equivalent chromosomic fragments in P. falciparum and Plasmodium knowlesi . (biomedcentral.com)
The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms. (biokeanos.com)
ConoServer is a database specializing in sequences and structures of peptides expressed by marine cone snails. (biokeanos.com)
The database gives access to protein sequences, nucleic acid sequences and structural information on conopeptides. (biokeanos.com)

Protein Homology/analogY Recognition Engine. (cicancer.org)
A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. (biomedcentral.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)
Comparative or homology modeling, which uses experimentally elucidated structures of related protein family members as templates, is currently the most accurate and reliable approach to model the structure of the protein of interest. (unibas.ch)
The SWISS-MODEL expert system developed by our group is a fully automated web-based workbench, which greatly facilitates the process of computing of protein structure homology models. (unibas.ch)
This would also help further refine homology modelling and molecular docking approaches, and better understand the structure-function relationships. (researchsquare.com)

Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development. (brenda-enzymes.org)
It was on that occasion that in a conversation with David Moss, Professor of Biomolecular Structures, and his co-worker Dr. Clare Sansom, the idea was conceived to organize the postgraduate course in bioinformatics, this newly emerging interdisciplinary research area as the interface between biological and computational sciences, primarily aimed at research students from Central and Eastern Europe. (iospress.nl)
Therefore computational prediction of protein features from their sequence is often used for designing strategies for experimental characterization of proteins and is also important for genome annotation and drug target identification [ 4 , 5 ]. (biomedcentral.com)
In particular, the computational prediction of subcellular location from protein sequence information has been attempted mainly using three approaches. (biomedcentral.com)
Computational protein structure prediction remains one of the most challenging problems in structural bioinformatics. (biomedcentral.com)
Prediction of the 3D structure of a protein from its amino acid sequence remains a fundamental scientific problem, and it is considered as one of the grand challenges in computational biology. (unibas.ch)
In this short review, we outline recent progresses in dissecting the conformational mechanisms of membrane proteins using HDX-MS. We further describe how the use of computational strategies can aid the interpretation of experimental data and enable visualisation of otherwise intractable membrane protein states. (silverchair.com)
An effective computational method incorporating multiple secondary structure predictions in topology determination for cryo-EM images. (odu.edu)
A number of computational tools for metabolism prediction have been developed over the last 20 years to predict the structures of small molecules undergoing biological transformation or environmental degradation. (biomedcentral.com)

This means that 2 adjacent residues in the primary structure must form the same hydrogen bonding pattern. (wikipedia.org)
These substitutions either create premature termination codons, which lead to truncated proteins, or substitute highly conserved residues in the bHLH region. (biomedcentral.com)
Since protein structural class prediction is a typical classification problem, we have developed a Support Vector Machine (SVM)-based method for protein structural class prediction that uses features derived from the predicted secondary structure and predicted burial information of amino acid residues. (bvsalud.org)
It suggests that such mutation might not effect the protein function although the both residues do not share very close phisicochemical properties. (tu-muenchen.de)
Information regarding solvent accessibility, molecular dynamics and energy minimization calculations showed that this variant causes clashes with neighboring amino acids residues that must interfere in the normal triple helix formation of trimeric subunit and further with the normal assembly of MBL oligomeric form, hence decrease in stability. (springeropen.com)

Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. (wikipedia.org)
We propose a new template-based modelling method called ThreaderAI to improve protein tertiary structure prediction. (biomedcentral.com)
Knowledge of the secondary structure and solvent accessibility of a protein plays a vital role in the prediction of fold, and eventually the tertiary structure of the protein. (edu.au)

In addition, some recent works such as [ 19 , 20 ] adopted structural information in other bioinformatics fields and the considerable performance gains indicate the huge potential of protein structural information. (biomedcentral.com)
There is a need for the development of highly accurate bioinformatics tools for predicting RNA binding function and protein-RNA complex structures. (buyresearchchemicalss.net)
To predict the possible impact of SNPs on MBL structure and function SNP data obtained from dbSNP database were analyzed using various bioinformatics tools. (springeropen.com)
An extensive bioinformatics analysis of the coronavirus replicase proteins by Snijder et al. (pdfroom.com)

The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. (biokeanos.com)

in 1951 (before any protein structure had ever been experimentally determined). (wikipedia.org)
One of the major limitations for using structure-based methods in biomedical research is the limited availability of experimentally determined protein structures. (unibas.ch)
It is difficult to locate RBPs and determine their protein-RNA complex structures experimentally due to high flexibility of RNA structures and the difficulty associated with crystallization of complex structures. (buyresearchchemicalss.net)
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. (biokeanos.com)

CUPSAT: prediction of protein stability upon point mutations. (brenda-enzymes.org)
CUPSAT is a tool to predict changes in protein stability upon point mutations. (brenda-enzymes.org)
CUPSAT uses protein environment specific mean force potentials to predict protein stability. (brenda-enzymes.org)

The Critical Assessment of Structure Prediction ( CASP ) experiment has for the last 25 years assessed the progress in the field of protein structure modeling. (unibas.ch)

Fragment libraires improved the accuracy of protein folding and outperformed state-of-the-art algorithms with respect to predicted properties, such as torsion angles and inter-residue distances. (biomedcentral.com)
Over the two decades that PredictProtein has been operating, we have substantially expanded the breadth of structural annotations, e.g. by adding predictions of non-regular secondary structure and intrinsically disordered regions, disulphide bridges and inter-residue contacts, and finally by also covering trans-membrane beta barrels structures. (bromberglab.org)
In this study we explored the relationship between residue exposure and protein subcellular location. (biomedcentral.com)
We developed a new algorithm for subcellular location prediction that uses residue exposure signatures. (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)
Predicted structural features include secondary structure (17) backbone torsion angles (16) and Pranoprofen residue solvent accessibility (18). (buyresearchchemicalss.net)
It encodes a 248 amino acid residue transmembrane protein, MBL (NCBI accession number XP_011538118.1) which is encoded via a 3570 bp long mRNA (NCBI accession number NM_000242.21). (springeropen.com)

Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. (wikipedia.org)
Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone. (wikipedia.org)
Secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. (wikipedia.org)
Other helices, such as the 310 helix and π helix, are calculated to have energetically favorable hydrogen-bonding patterns but are rarely observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix. (wikipedia.org)

A combination of fluorescence microscopy, neutron reflectometry, and time-of-flight secondary-ion mass spectrometry data will be presented which characterizes the structure and composition of this new supported lipid bilayer category. (lu.se)

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)
This module predicts stabilty changes upon point mutation from a PDB structure. (brenda-enzymes.org)

Fold recognition, assigning novel proteins to known structures, forms an important component of the overall protein structure discovery process. (bvsalud.org)
The available methods for protein fold recognition are limited by the low fold-coverage and/or low prediction accuracies. (bvsalud.org)
We describe here a new Support Vector Machine (SVM)-based method for protein fold prediction with high prediction accuracy and high fold-coverage. (bvsalud.org)
The new method of fold prediction with high fold-coverage was developed by training and testing on a large number of folds in order to make the method suitable for large scale fold predictions. (bvsalud.org)
In order to overcome this complexity we adopted a hierarchical approach where fold-prediction is made in two steps. (bvsalud.org)
This decreased the complexity of the classification problem and also improved the overall fold prediction accuracy. (bvsalud.org)
To the best of our knowledge this is the first taxonomic fold recognition method to cover over 700 protein-folds and gives prediction accuracy of around 70% on a benchmark dataset. (bvsalud.org)
More specifically SPOT-Seq-RNA employs a template library of non-redundant protein-RNA complex structures and attempts to match the query sequence to the protein structures in protein-RNA complexes by the fold recognition technique SPARKS X (12). (buyresearchchemicalss.net)
Extensive 10-fold cross-validation and independent tests demonstrated that TIMER achieves a competitive performance and outperforms several existing methods on both general and species-specific promoter prediction. (giwebb.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)

Since the new method gives rise to state of the art prediction performance and hence can be very useful for structural characterization of proteins discovered in various genomes. (bvsalud.org)
Unfortunately, somewhat less effort has been devoted to the characterization or understanding of non-essential or secondary metabolism and non-essential metabolites, partly due to their much higher number, and greater structural complexity, compared to primary metabolites. (biomedcentral.com)

The TWIST1 protein is highly conserved from Drosophila to humans, where it plays a key role during embryonic morphogenesis, mesoderm patterning and development. (biomedcentral.com)
Three dimensional structure is highly conserved in protein evolution1. (researchsquare.com)

However, most current approaches used for functional annotation simply focus on the use of protein-level information but ignore inter-relationships among annotations.Here, we established PFresGO, an attention-based deep-learning approach that incorporates hierarchical structures in Gene Ontology (GO) graphs and advances in natural language processing algorithms for the functional annotation of proteins. (giwebb.com)
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. (biokeanos.com)

We have also added important resources for the prediction of protein function, e.g. assisting in the annotation of subcellular localization (LocTree, LocTree2, NLSpred), identifying protein-protein interaction sites (ISIS) and protein-DNA binding sites (DISIS & SomeNA to be released shortly). (bromberglab.org)

Hydrogen bonding patterns in secondary structures may be significantly distorted, which makes automatic determination of secondary structure difficult. (wikipedia.org)
The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. (wikipedia.org)
Structural information, where available, has been employed by several available tools (COMPARER17, STAMP18, and GAFIT19), which often recruit structural features such as secondary structural, solvent burial and hydrogen bonding patterns to recognize the structural core and variable regions to guide the presence of gaps and to obtain reliable alignments. (researchsquare.com)

The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. (wikipedia.org)
The most common secondary structures are alpha helices and beta sheets. (wikipedia.org)

NetSurfP-2.0 is sequence-based and uses an architecture composed of convolutional and long short-term memory neural networks trained on solved protein structures. (ku.dk)
block: questionnaire reform type selling Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. (wyodoug.com)
Large-Scale Prediction of Disulphide Bridges looking Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching. (wyodoug.com)
Reaction: competition download relief shutting Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks. (dl-mirror-art-design.de)

Structural Analysis and Prediction of Protein Mutant Stability using Distance and Torsion Potentials: Role of Secondary Structure and Solvent Accessibility. (brenda-enzymes.org)
Fragment libraries contain rich structural information, including 1D structural properties such as secondary structure and torsion angles, and 2D structural properties such as distances and orientations between pairs of heavy atoms. (biomedcentral.com)
The prediction model uses amino acid-atom potentials and torsion angle distribution to assess the amino acid environment of the mutation site. (brenda-enzymes.org)
Gaussian apodisation function has been used to accomodate torsion angle perturbation in protein mutants. (brenda-enzymes.org)
Torsion angle information and details of Accessible Surface Area & Secondary structure specificity of the given amino acid environment are provided (DSSP). (brenda-enzymes.org)

Recent advances in the methodology and instrumentation have enabled the application of HDX-MS to membrane proteins. (silverchair.com)
Developing new tools are therefore pertinent for improving our fundamental knowledge of how membrane proteins function in the cell. (silverchair.com)
Membrane proteins play critical roles in higher organisms and are responsible for diverse cellular functions such as signalling and molecular transport. (silverchair.com)
Native membrane derived polymer-supported lipid bilayers (nSLBs) are poised to bridge the gap between live cell experiments and traditional model membrane architectures that by offering a combination of accessibility by surface sensitive analytical instrumentation and a composition which more closely resembles cellular membranes by displaying a diversity of endogenous membrane proteins, lipids, and carbohydrates. (lu.se)

We review methods for the detection of correlated amino acid substitutions, compare their relative performance in contact prediction and predict future directions in the field. (unimi.it)

Given that the energy potentials are mainly derived from the predicted protein properties, the accuracy of the predicted protein properties, to a large extent, determines the quality of final predicted structures. (biomedcentral.com)

We broadened the usage of such structural information by transforming fragment libraries into protein-specific potentials for gradient-descent based protein folding and encoding fragment libraries as structural features for protein property prediction. (biomedcentral.com)
Recently, we have developed an approach for dynamically combining the knowledge-based statistical potentials of QMEAN with distance constraints derived from homologous template structures (QMEANDisCo). (unibas.ch)

There are several methods for formally defining protein secondary structure (e.g. (wikipedia.org)
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)
The main interest of our group is the development of methods and algorithms for molecular modeling and simulations of three-dimensional protein structures and their interactions. (unibas.ch)
Methods for structure modeling and prediction have made substantial progress over the last decades, but still fall short in accuracy compared to high-resolution experimental structures. (unibas.ch)
A blind test on the EVA dataset gives an average Q3 accuracy of 74.5% and ranks in top five protein structure prediction methods. (edu.au)
However, relatively high levels of false-positive predictions typically render such methods, in isolation, of little use in the ab initio prediction of protein structure. (unimi.it)
Structural MS has emerged as a powerful tool for characterising protein structure and function, complementing high-resolution methods [ 7-9 ]. (silverchair.com)

HDX-MS has emerged as a powerful tool to interrogate the structure and dynamics of proteins and their complexes. (silverchair.com)
Understanding the mechanism underpinning membrane-related function requires detailed characterisation of membrane protein structure and dynamics. (silverchair.com)
Other emerging structural techniques such as pulsed electron double resonance (PELDOR or DEER) have contributed invaluable insights into membrane protein structural dynamics [ 4-6 ]. (silverchair.com)
While powerful, native MS alone, offers little information on protein dynamics. (silverchair.com)
HDX-MS, on the other hand, provides an extremely sensitive method for interrogating the conformational dynamics of proteins and their complexes via monitoring the exchange of hydrogens to deuterium [ 17-19 ]. (silverchair.com)
versatile dynamics lie that dry rule of the nitromethane and long protein Investigated triggered by the account to exceed with hydrodynamic file, well otherwise to start and tune our simulations, but to be center of the velocities of structural thinking. (sojars593.org)
Whereas a recent MD simulation indi- cates that the structure of the cavity water resembles a bulk water droplet, the present MRD results show that its dynamics is more than two orders of magnitude slower than in the bulk. (lu.se)
While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)

The structural analysis shows that the mutated site is exposed and has a coil secondary structure on the domain region. (tu-muenchen.de)
Protein structural analysis with this amino acid variant was performed by using I-TASSER, RAMPAGE, Swiss-PdbViewer, Chimera and I-mutant. (springeropen.com)

The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). (biokeanos.com)

Such features, when coupled with carefully designed algorithms, lead to good predictions empirically. (biomedcentral.com)
Ranjan, D. "ABI Innovation: Advanced Informatics and Eective Algorithms for Improved CryoEM Protein Structure Prediction and Density Analysis" $589,703. (odu.edu)

The top-five peptide model offered ideal prediction with high accuracy (Q(2)=0.99916). (cdc.gov)

Accurate sequence alignments of distantly related proteins are crucial for the better understanding of proteins at their family/superfamily level. (researchsquare.com)
However, such alignments of distantly related proteins are often hard to obtain by automatic multiple sequence alignment programs. (researchsquare.com)
This protocol employs two stages of structure-based sequence alignments in order to obtain reliable alignments. (researchsquare.com)
We further propose a novel assessment of the derived alignments using the measurements of the structural variations and the percentage secondary structural equivalences. (researchsquare.com)
We have earlier shown that the large-scale alignments of several protein domain superfamilies are possible by resorting to structure-based sequence alignment methods13-15. (researchsquare.com)
The availability of accurate structure-based sequence alignments of protein families and superfamilies is crucial to inferring their evolutionary relationships, functional properties4 and to understand the structural variances between the different classes of proteins. (researchsquare.com)
Rapid structure-based sequence alignments employ a comparison of the orientations of the secondary structures (Murthy20, SSAP7,21, and SEA22 programs) or hexapeptide fragments (DALI5,6) to recognize accurate alignments of protein domains that belong to the same superfamilies. (researchsquare.com)

Established in 1965, the Cambridge Structural Database (CSD) is the a repository for small-molecule organic and metal-organic crystal 3D structures. (biokeanos.com)
BioTransformer combines a machine learning approach with a knowledge-based approach to predict small molecule metabolism in human tissues (e.g. liver tissue), the human gut as well as the environment (soil and water microbiota), via its metabolism prediction tool. (biomedcentral.com)

NetPhos (phosphorylation in eukariotic proteins). (cicancer.org)
NetPhosK (kinase specific phosphorylation in eukariotic proteins). (cicancer.org)
BTK, a TEC-family tyrosine kinase activated by the B-cell antigen receptor, contains a variety of regulatory domains and it is subject to complex regulation by membrane phospholipids, protein ligands, phosphorylation, and dimerization. (elifesciences.org)

One approach tries to identify motifs recognized by the sorting proteins and receptors of the protein transport machinery to move protein products from the cytosol to other subcellular locations [ 6 ]. (biomedcentral.com)

Thus locating all RNA-binding proteins (RBPs) in a genome and determining protein-RNA complex structures are key steps for understanding the mechanism of post-transcriptional regulation and for mapping the network of protein-RNA interactions. (buyresearchchemicalss.net)
Protein structure comparison also helps to improve tools for identifying gene functions in genome databases by defining the essential sequence-structure features of a protein family16. (researchsquare.com)

EnzymeDetector: an integrated enzyme function prediction tool and database. (brenda-enzymes.org)
The ability to predict local structural features of a protein from the primary sequence is of paramount importance for unraveling its function in absence of experimental structural information. (ku.dk)
Another major addition are the tools that predict the effect of amino acid changes upon protein function (SNAP & SNAP2), and directly upon protein structure (in preparation). (bromberglab.org)
Therefore, the study of protein function can be facilitated by predictions of protein location. (biomedcentral.com)
The cell's functional machinery - proteins - need to be present at specific cellular compartments so that cells can function properly. (biomedcentral.com)
Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. (biomedcentral.com)
To this end, we have introduced the composite scoring function QMEAN, which consists of four statistical potential terms and two components describing the agreement between predicted and observed secondary structure and solvent accessibility. (unibas.ch)
For binding affinity prediction we extracted a knowledge-based energy function DRNA from protein-RNA complex structures (19) based on a distance-scaled finite ideal-gas reference (DFIRE) state (20). (buyresearchchemicalss.net)
While high resolution structures of membrane nanomachines are undeniably pertinent, our ability to leverage structure against function, requires us to have access to their conformational changes and functional states. (silverchair.com)
As a GTPase-activating protein, a key function of Nf1 is repression of the Ras oncogene signalling cascade. (nature.com)
Substituting alanine, which is small and unpolar, by the long and acidic aspartate might also impact the structure and function of the protein. (tu-muenchen.de)
nsSNPs may affect the protein function by reducing protein solubility or by destabilizing protein structure (Chasman and Adams 2001 ). (springeropen.com)
Wolfram syndrome type 1 gene ( WFS1 ), which encodes a transmembrane structural protein (wolframin), is essential for several biological processes, including proper inner ear function. (biomedcentral.com)
Sweden ties must be important for protein function. (lu.se)

Despite this difficulty there is a steady increase in the number of protein-RNA complex structures deposited in the protein data bank from 45 in 2001 Pranoprofen to 180 in 2011 (non-redundant at 90% sequence identity or less) (1). (buyresearchchemicalss.net)

Two main factors affect the utility of potential prediction tools: their accuracy must enable extraction of reliable structural information on the proteins of interest, and their runtime must be low to keep pace with sequencing data being generated at a constantly increasing speed. (ku.dk)
We assessed the accuracy of NetSurfP-2.0 on several independent test datasets and found it to consistently produce state-of-the-art predictions for each of its output features. (ku.dk)
In addition to improved accuracy, the processing time has been optimized to allow predicting more than 1000 proteins in less than 2 hours, and complete proteomes in less than 1 day. (ku.dk)
Calibration of the method using predicted values of amino acid exposure allows classifying proteins without 3D-information with an accuracy of 62% and discerning proteins in different locations even if they shared high levels of identity. (biomedcentral.com)
The model accuracy of TBM method critically depends on protein features and the scoring functions that integrate these features. (biomedcentral.com)
The examination of different individual as well as feature combinations revealed that the combination of secondary structural content, secondary structural and solvent accessibility state frequencies of amino acids gave rise to the best leave-one-out cross-validation accuracy of ~81% which is comparable to the best accuracy reported in the literature so far. (bvsalud.org)

Protein Mutant stAbilitY Analyzer. (cicancer.org)
Mutant stability predictions from PDB as well as custom developed protein structures are possible. (brenda-enzymes.org)
If you like to use an alternative model, extract the model (copy and paste from MODEL to ENDMDL) to a new file and use the module Predict Mutant Stability from Custom Protein Structures . (brenda-enzymes.org)

Here, an overview of the publicly available knowledge about IDRs is reported, including manually curated resources, deposition databases and prediction repositories. (iucr.org)

QMEANBrane further extends the approach to membrane protein structures, which play crucial roles in many biological processes and are important drug targets. (unibas.ch)
The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. (biokeanos.com)
The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules. (biokeanos.com)

TWIST1 proteins can form either homodimeric (TWIST1/TWIST1) or heterodimeric complexes, mainly in association with E2A proteins. (biomedcentral.com)

Amino acids vary in their ability to form the various secondary structure elements. (wikipedia.org)

Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)

The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. (elifesciences.org)
Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. (elifesciences.org)
Structures of the autoinhibited SRC family kinases were solved in 1997 revealing, for the first time, the compact arrangement of the SH3 and SH2 domains assembled onto the distal side of the catalytic kinase domain [ 4 ]. (elifesciences.org)
The compact structure of the SH3-SH2-kinase region of BTK is exacted from the domain swapped dimer structure (PDB: 4XI2) solved by Wang et al. (elifesciences.org)
Furthermore, the kinase and SAM domains allow the binding of other cellular proteins. (genominfo.org)

Our work implies that the rich structural information extracted from fragment libraries can complement sequence-derived features to help protein structure prediction. (biomedcentral.com)
However, those features only leverage sequential information, and incorporating new features from known protein structures could serve as a complement and thus benefit protein property predictions. (biomedcentral.com)
To identify such inaccuracies, scoring functions have been developed which analyze different structural features of the protein models in order to derive a quality estimate. (unibas.ch)
Initially, given PDB file is analyzed for its atom environment & secondary structure features. (brenda-enzymes.org)
The majority of this work uses machine learning to predict protein structural and functional features. (giwebb.com)

This structure-based sequence alignment protocol can be employed for a single superfamily or for a large number of structural domain superfamilies in a near-automatic and rapid manner. (researchsquare.com)

We observe a correlation of 80% between predictions and experimental data for solvent accessibility, and a precision of 85% on secondary structure 3-class predictions. (ku.dk)

Since protein structures have a much higher degree of conservation than the sequences2, comparison of protein structures may reveal distant evolutionary relationships that would not be detected from sequence information alone3,4. (researchsquare.com)

Ranjan, D. "Phylogenetic predictions of the capabilities of novel biothreat agents" $135,000. (odu.edu)
50% protein identity with its phylogenetic relatives of the genus Copiparvovirus . (cdc.gov)

To address these limitations, we have developed BioTransformer, a freely available software package for accurate, rapid, and comprehensive in silico metabolism prediction and compound identification. (biomedcentral.com)

Anatomy4

Organisms5

Chemicals and Drugs76

Analytical, Diagnostic and Therapeutic Techniques and Equipment64

Phenomena and Processes82

Disciplines and Occupations12

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture6

Information Science35

Health Care18

Nucleic acids3

Sequences16

Homology7

Computational9

Residues5

Tertiary structure3

Bioinformatics4

Intrinsically disordered proteins1

Experimentally4

CUPSAT3

Critical Assessment of Structure Prediction1

Residue7

Backbone4

Mass spectrometry data1

Predicts2

Fold11

Characterization2

Highly conserved2

Functional annotation2

Annotation1

Hydrogen bonding3

Helices2

Neural networks4

Torsion5

Membrane proteins4

Contact prediction1

Derived from the predicted1

Potentials2

Methods8

Dynamics8

Structural Analysis2

Molecular1

Algorithms2

Peptide1

Alignments7

Small-molecule2

Phosphorylation3

Subcellular1

Genome2

Function14

Sequence identity1

Accuracy6

Mutant3

Manually curated1

Biological3

Complexes1

Amino acids1

Fixed three-dimensional1

Kinase5

Features5

Superfamily1

Experimental data1

Evolutionary relationships1

Phylogenetic2

Silico1