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A comparative account of protein-protein interaction resources, feature-validations and application-based categorizations : PPIs of plants proteins
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
AraNet - Probabilistic Functional Gene Network of Arabidopsis thaliana
A resource of interactions in plant proteins (Arabidopsis thaliana). Provides both experimental & predicted interactions. Provides interactions based on the proteins' sequence conservation/similarity. Provides functional associations for the interactions. Provides the pathway and other proteins involved, along with the interactions, for a given set of proteins. Predicted interaction based on gene expression. Provides interactions along with their functional associations. Interactions can be restricted to a given experimental evidence.
Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol. 2010 Feb;28(2):149-56. Epub 2010 Jan 31. PubMed PMID: 20118918; PubMed Central PMCID: PMC2857375.
AtPID - Arabidopsis thaliana Protein Interactome Database
A database of interactions in plant proteins (Arabidopsis thaliana). Provides predicted interactions based on gene expression, genomic data, Gene Ontology terms, orthology. Provides domain interactions. Provides functional associations for the interactions.
Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T. AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res. 2008 Jan;36(Database issue):D999-1008. Epub 2007 Oct 25. PubMed PMID: 17962307; PubMed Central PMCID: PMC2238993.
URL could not be retrieved (20/12/2011).
MiMI - Michigan Molecular Interaction
Collects protein interaction data from multiple PPI databases. Provides interactions along with their functional associations.
Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35(Database issue):D566-71. Epub 2006 Nov 27. PubMed PMID: 17130145; PubMed Central PMCID: PMC1716720.
MINT - Molecular INTeraction
A database that provides PPIs of experimental importance. It also identifies interactions among the given list of proteins. Provides options to curate data for the database.
Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. MINT: a Molecular INTeraction database. FEBS Lett. 2002 Feb 20;513(1):135-40. Review. PubMed PMID: 11911893.
MitoInteractome - Mitochondrial Protein Interactome Database
A resource specific to mitochondrial PPIs. Predicts interactions based on the domain/interfaces/sites. Provides inferred interactions (e.g., human interactions inferred from mouse & rat).
Reja R, Venkatakrishnan AJ, Lee J, Kim BC, Ryu JW, Gong S, Bhak J, Park D. MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. BMC Genomics. 2009 Dec 3;10 Suppl 3:S20. PubMed PMID: 19958484; PubMed Central PMCID: PMC2788373.
PINT - Protein-protein Interactions Thermodynamic
A resource that provides the kinetics/thermodynamics of the interactions. Considers only PubMed for retrieving PPIs. Provides options for uploading or submitting the interaction data.
Kumar MD, Gromiha MM. PINT: Protein-protein Interactions Thermodynamic Database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D195-8. PubMed PMID: 16381844
URL could not be retrieved (20/12/2011). License is required for commercial use
STRING - Search Tool for the Retrieval of Interacting Genes/Proteins
A database that predicts protein-interactions based on co-expression, genomic data, gene fusion. Also collects PPIs from multiple databases. Provides information on the function of interactions. Can also query with multiple genes/proteins.
Snel B, Lehmann G, Bork P, Huynen MA. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 2000 Sep 15;28(18):3442-4. PubMed PMID: 10982861; PubMed Central PMCID: PMC110752.
copyright © Dr. Kshitish Acharya K; all rights reserved

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