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Links tagged with 'protein interaction domains and motifs'

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3didDatabase Content

http://3did.irbbarcelona.org/

Protein > Databases

The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server visualizes these interfaces along with atomic details of individual interactions using Jmol.

NAR Database Issue 2011
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tagsmolecular models peptides protein databases protein interaction domains and motifs protein interaction mapping

d-OmixTool Content

http://www.biotec.or.th/isl/Domix

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.

NAR Web Server Issue 2009
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tagsphylogeny protein interaction domains and motifs proteins proteomics tertiary protein structure

DASMIwebDatabase Content

http://www.dasmiweb.de

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Retrieval

The DASMIweb server allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can support incorporation of user data.

NAR Web Server Issue 2009
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tagsonline systems protein interaction domains and motifs protein interaction mapping systems integration

DIMA 3.0Database Content

http://webclu.bio.wzw.tum.de/dima

Protein > Databases

Domain Interaction MAp (DIMA) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

NAR Database Issue 2011
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tagsmutation protein databases protein interaction domains and motifs protein interaction mapping

DOMINEDatabase Content

http://domine.utdallas.edu

Protein > Databases

DOMINE is a collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. The updated DOMINE includes 2285 new domain-domain interactions (DDIs) inferred from experimentally characterized high-resolution three-dimensional structures, and about 3500 novel predictions by five computational approaches published over the last 3 years. New features include a new classification scheme to assign confidence levels to predicted DDIs.

NAR Database Issue 2011
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tagsprotein databases protein interaction domains and motifs protein interaction mapping

HitPredictDatabase Content

http://hintdb.hgc.jp/htp/

Protein > Databases

HitPredict is a database with quality assessed PPIs in nine species. HitPredict assigns a confidence level to interactions based on a reliability score that is computed using evidence from sequence, structure and functional annotations of the interacting proteins.

NAR Database Issue 2011
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tagsprotein databases protein interaction domains and motifs protein interaction mapping

iRefIndexDatabase Content

http://irefindex.uio.no/wiki/iRefIndex

Protein > Interactions, Pathways, Enzymes

iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.

This content is being maintained by ian.donaldson.

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tagsamino acid sequence analysis of variance animals computational biology data compression data display database management systems humans neural networks (computer) protein databases protein interaction domains and motifs protein interaction mapping protein isoforms proteins proteome proteomics

PCFamilyTool Content

http://pcfamily.life.nctu.edu.tw

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes

The PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.

NAR Web Server Issue 2010
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tagserythropoietin erythropoietin receptors multiprotein complexes protein binding protein interaction domains and motifs protein sequence analysis protein structural homology s-phase kinase-associated proteins

PPISearchTool Content

http://gemdock.life.nctu.edu.tw/ppisearch/

Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Similarity Searching

PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.

NAR Web Server Issue 2009
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tagsadaptor protein complex 1 amino acid sequence homology animals caenorhabditis elegans proteins mice protein databases protein interaction domains and motifs protein interaction mapping

PredUsTool Content

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PredUs

Protein > Interactions, Pathways, Enzymes

PredUs is a web server for the prediction of protein-protein interfaces. The method predicts protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors.

This content is being maintained by cliffzhang.

NAR Web Server Issue 2011
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tagsalgorithms artificial intelligence binding sites computational biology conserved sequence molecular models multiprotein complexes protein binding protein conformation protein databases protein interaction domains and motifs protein interaction mapping protein structural homology proteins sequence alignment surface properties systems biology

ProtCIDDatabase Content

http://dunbrack2.fccc.edu/protcid

Protein > Databases

The protein common interface database (ProtCID) is a database that contains clusters of similar homodimeric and heterodimeric interfaces observed in multiple crystal forms (CFs). In ProtCID, protein chains in the protein data bank (PDB) are grouped based on their PFAM domain architectures. For a single PFAM architecture, all the dimers present in each CF are constructed and compared with those in other CFs that contain the same domain architecture. Interfaces occurring in two or more CFs comprise an interface cluster in the database. The same process is used to compare heterodimers of chains with different domain architectures. Our data therefore provide an independent check on publicly available annotations of the structures of biological interactions for PDB entries. Coordinates for all interfaces in a cluster are downloadable for further analysis.

This content is being maintained by dunbrack.

NAR Database Issue 2011
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tagsamino acid sequence homology dimerization molecular models phylogeny protein databases protein interaction domains and motifs protein interaction mapping proteins x-ray crystallography