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PDZBase specifications

Information


Unique identifier OMICS_02952
Name PDZBase
Restrictions to use None
Maintained Yes

Publication for PDZBase

PDZBase citations

 (6)
library_books

The Identification of Specific Methylation Patterns across Different Cancers

2015
PLoS One
PMCID: 4361543
PMID: 25774687
DOI: 10.1371/journal.pone.0120361

[…] oteins (DIP), the Human Protein Reference Database (HPRD), IntAct, the Molecular IN Teraction database (MINT), the mammalian PPI database of the Munich Information Center on Protein Sequences (MIPS), PDZBase (a PPI database for PDZ-domains) and Reactome[–]. Because many experimental factors might influence the result of PPI network, which led to the repeatable interactions in PPI network, we integ […]

library_books

Proteomics Analysis of the Non Muscle Myosin Heavy Chain IIa Enriched Actin Myosin Complex Reveals Multiple Functions within the Podocyte

2014
PLoS One
PMCID: 4065073
PMID: 24949636
DOI: 10.1371/journal.pone.0100660

[…] -protein interactions (PPIs) from publicly available sources including the following databases and publications: BioGrid , HPRD , InnateDB , IntAct , KEGG , KEA , MINT , MIPS , DIP , BIND , BioCarta, PDZBase and PPID –. For the pathway enrichment analysis we used Lists2Networks to compute enrichment for BioCarta pathways, Gene Ontology , WikiPathways , as well as several other gene set libraries […]

library_books

A Dynamic View of Domain Motif Interactions

2012
PLoS Comput Biol
PMCID: 3257277
PMID: 22253583
DOI: 10.1371/journal.pcbi.1002341

[…] We extracted human domain-motif interactions from seven databases (PepCyber , Uniprot , DOMINO , ELM , PDZbase and 3DID ) and integrated them into one unified catalogue of 2,683 such interactions. First, we filtered the database to include only interactions with motifs that are 30 residues or shorter. […]

library_books

PDZ domains and their binding partners: structure, specificity, and modification

2010
PMCID: 2891790
PMID: 20509869
DOI: 10.1186/1478-811X-8-8

[…] rce to investigate biological networks and signaling pathways within cells [-,-]. This information needs to be comprehensively deposited in publicly available repositories, such as iSPOT, DOMINO, and PDZBase [-], in order to maximally accelerate the discovery of novel PDZ-mediated interactions in cells. PDZBase is a unique database that contains information extracted from the literature of all kno […]

library_books

Minimotif miner 2nd release: a database and web system for motif search

2008
Nucleic Acids Res
PMCID: 2686579
PMID: 18978024
DOI: 10.1093/nar/gkn865

[…] ist for minimotifs. Rather short contiguous functional motifs are generally catalogued by functional groupings and dispersed over a collection of specialized databases such as MEROPS, Phosphobase and PDZbase (). Minimotif Miner (MnM) contains a broader set of minimotifs allowing analysis of many different types of minimotifs in a single query (). Through minimotif prediction, MnM provides the mean […]

library_books

An evaluation of human protein protein interaction data in the public domain

2006
BMC Bioinformatics
PMCID: 1764475
PMID: 17254303
DOI: 10.1186/1471-2105-7-S5-S19

[…] PDZBase is a database that focuses only on PPIs involving proteins with PDZ domains [,]. Only those interactions involving the PDZ domain that have been confirmed by individual in vitro or in vivo bio […]

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PDZBase institution(s)
Department of Physiology and Biophysics, Weill Medical College of Cornell University; New York, NY, USA

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