> Tag > Links tagged with 'protein conformation'

Links tagged with 'protein conformation'

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Found 159 links

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BRENDA - The Comprehensive Enzyme Information SystemDatabase Content

http://www.brenda-enzymes.org/ [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.

links directory index: 792
TitlePublication YearGoogle Scholar Citation Count
BRENDA, AMENDA and FRENDA: the enzyme information system in 20072007115
BRENDA, the enzyme database: updates and major new developments2004347
BRENDA: a resource for enzyme data and metabolic information2002104
BRENDA, enzyme data and metabolic information2002226
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tagsanimals enzymes factual databases genomics humans ligands membrane proteins organ specificity protein conformation protein databases protein transport rats substrate specificity systems integration terminology as topic

BriXDatabase Content

http://brix.crg.es [open in a new window]

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Protein > Databases

BriX is a vast database of protein fragments, clustered on their backbone similarity. BriX contains fragments from 7290 proteins from the Astral40 set, fragmented in lengths ranging from 4 to 14 amino acids and clustered against 6 different distance thresholds on similarity of the protein backbone. Loop BriX contains loop fragments from 14.525 proteins from the Astral95 set, clustered according to end-to-distance and anchor residue superposition.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
BriX: a database of protein building blocks for structural analysis, modeling and design20114
NAR Database Issue 2011
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tagsmolecular models protein conformation protein databases proteins

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching and Classification

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains20068
Assessment of a rigorous transitive profile based search method to detect remotely similar proteins200510
NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

CASTpTool Content

http://sts.bioengr.uic.edu/castp/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

links directory index: 1616
TitlePublication YearGoogle Scholar Citation Count
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues2006372
CASTp: Computed Atlas of Surface Topography of proteins2003264
Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins1998153
Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape1998226
Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design1998601
NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

CDDBDatabase Content

http://www.cdyn.org [open in a new window]

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Protein > Databases

The conformational dynamics data bank (CDDB) is a database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies20112
NAR Database Issue 2011
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tagsmultiprotein complexes protein conformation protein databases proteins

CLICKTool Content

http://mspc.bii.a-star.edu.sg/click [open in a new window]

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Protein > 3-D Structure Comparison

CLICK web server is a topology independent method of comparison of biomolecular 3D structures.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
CLICK--topology-independent comparison of biomolecular 3D structures20112
NAR Web Server Issue 2011
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tagsalgorithms molecular conformation molecular models nucleic acid conformation protein conformation rna

ClotbaseDatabase Content

http://www.clotbase.bicnirrh.res.in/ [open in a new window]

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Protein > Databases

ClotBase is a curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases , mutation and links to external databases

links directory index: 0
TitlePublication YearGoogle Scholar Citation Count
ClotBase: a knowledgebase on proteins involved in blood coagulation.20100
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tagsamino acid sequence animals blood coagulation blood coagulation disorders blood coagulation factors blood proteins consensus sequence factual databases genetic databases humans molecular sequence data mutation mutation prediction mutations protein conformation protein databases proteins sequence alignment

ClusProTool Content

http://cluspro.bu.edu/login.php [open in a new window]

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Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

links directory index: 511
TitlePublication YearGoogle Scholar Citation Count
Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19201033
PIPER: an FFT-based protein docking program with pairwise potentials2006100
ClusPro: an automated docking and discrimination method for the prediction of protein complexes2004247
ClusPro: a fully automated algorithm for protein-protein docking2004131
NAR Web Server Issue 2004
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tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

Combinatorial Extension of the Optimal PathDatabase Content

http://cl.sdsc.edu/ce.html [open in a new window]

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Protein > 3-D Structure Comparison

Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.

links directory index: 1542
TitlePublication YearGoogle Scholar Citation Count
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path19981542
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tagsalgorithms amino acid sequence amino acid sequence homology molecular sequence data monte carlo method protein conformation protein folding proteins sequence alignment

ComSinDatabase Content

http://antares.protres.ru/comsin/. [open in a new window]

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Protein > Databases

ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder20108
NAR Database Issue 2010
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tagsanimals bacterial proteins computational biology genetic databases humans molecular conformation molecular models protein binding protein conformation protein databases tertiary protein structure

CSpritzTool Content

http://protein.bio.unipd.it/cspritz/ [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

CSpritz is a web server for the prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.

This content is being maintained by silvio.tosatto@unipd.it.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs20113
NAR Web Server Issue 2011
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tagsamino acid motifs molecular sequence annotation protein conformation protein structural homology secondary protein structure

DAnCERDatabase Content

http://wodaklab.org/dancer/ [open in a new window]

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DNA > Databases

The DAnCER (Disease Annotated Chromatin Epigenetic Resource) resource integrates information on genes with chromatin modification (CM) function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. DAnCER allows visual explorations of the integrated data and flexible query capabilities using a variety of data filters. In particular, disease information and functional annotations are mapped onto the protein interaction networks.

This content is being maintained by shoshana Wodak.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
DAnCER: disease-annotated chromatin epigenetics resource20115
NAR Database Issue 2011
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tagsanimals caenorhabditis elegans chromatin disease drosophila melanogaster epigenomics genetic databases humans mice molecular sequence annotation protein conformation protein interaction mapping saccharomyces cerevisiae

DBCPTool Content

http://120.107.8.16/dbcp [open in a new window]

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Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

The Disulfide Bonding Connectivity Pattern (DBCP) web server tool provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide bridges and helping to solve protein folding.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
DBCP: a web server for disulfide bonding connectivity pattern prediction without the prior knowledge of the bonding state of cysteines20107
NAR Web Server Issue 2010
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tagscysteine disulfides protein conformation protein folding protein sequence analysis proteins reproducibility of results

DEPTHTool Content

http://mspc.bii.a-star.edu.sg/depth [open in a new window]

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Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins20112
NAR Web Server Issue 2011
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tagsamino acids binding sites ligands molecular models peptide hydrolases protein conformation proteins west nile virus

DiANNATool Content

http://bioinformatics.bc.edu/clotelab/DiANNA/ [open in a new window]

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Protein > Biochemical Features
Protein > Sequence Features

DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.

links directory index: 89
TitlePublication YearGoogle Scholar Citation Count
DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification200625
DiANNA: a web server for disulfide connectivity prediction200564
Disulfide connectivity prediction using secondary structure information and diresidue frequencies.20050
NAR Web Server Issue 2005NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence binding sites chemical models computer simulation cysteine disulfides neural networks (computer) oxidation-reduction protein binding protein conformation protein interaction mapping protein sequence analysis proteins secondary protein structure sequence alignment structure-activity relationship

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