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APID: Agile Protein Interaction DataAnalyzer.

Nucleic acids research | Jul 1, 2006

Agile Protein Interaction DataAnalyzer (APID) is an interactive bioinformatics web tool developed to integrate and analyze in a unified and comparative platform main currently known information about protein-protein interactions demonstrated by specific small-scale or large-scale experimental methods. At present, the application includes information coming from five main source databases enclosing an unified sever to explore >35 000 different proteins and 111 000 different proven interactions. The web includes search tools to query and browse upon the data, allowing selection of the interaction pairs based in calculated parameters that weight and qualify the reliability of each given protein interaction. Such parameters are for the 'proteins': connectivity, cluster coefficient, Gene Ontology (GO) functional environment, GO environment enrichment; and for the 'interactions': number of methods, GO overlapping, iPfam domain-domain interaction. APID also includes a graphic interactive tool to visualize selected sub-networks and to navigate on them or along the whole interaction network. The application is available open access at http://bioinfow.dep.usal.es/apid/.

Pubmed ID: 16845013 RIS Download

Mesh terms: Computational Biology | Databases, Protein | Internet | Protein Interaction Mapping | Software | User-Computer Interface

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This is a list of tools and resources that we have found mentioned in this publication.


UniProt

Resource for protein sequence and functional information that welcomes updates, corrections, and the submission of new protein sequence data. It is comprised of four components, each optimized for different uses. UniProt Knowledgebase (UniProtKB) is the central access point for curated protein information, including function, classification, and cross-reference, and contains two sections: UniProtKB/Swiss-Prot, which is manually annotated and reviewed; and UniProtKB/TrEMBL, which is automatically annotated and not reviewed. UniProt Reference Clusters (UniRef) are databases providing clustered sets of sequences from the UniProtKB and selected UniProt Archive records to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences. UniProt Archive (UniParc) is a comprehensive repository used to keep track of sequences and their identifiers. UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data.

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PubMed

A bibliographic database that provides access to over 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include the fields of biomedicine and health, covering portions of the life sciences, behavioral sciences, chemical sciences, and bioengineering. PubMed also provides access to additional relevant web sites and links to the other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to the full-text of articles at journal web sites using LinkOut.

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InterPro

Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries.

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IntAct

Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available.

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