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PeptiSite: a structural database of peptide binding sites in 4D.

Abstract：

:We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include: (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a multimeric protein assembly with cofactors and metal ions and (3) analysis of consensus interaction motifs within the ensembles and identification of conserved determinants of these interactions. Currently the database contains 585 proteins with 650 peptide-binding sites. http://peptisite.ucsd.edu/ link allows searching for the sites of interest and interactive visualization of the ensembles using the ActiveICM web-browser plugin. This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark.

journal_name

Biochem Biophys Res Commun

journal_title

Biochemical and biophysical research communications

authors

Acharya C,Kufareva I,Ilatovskiy AV,Abagyan R

doi

10.1016/j.bbrc.2013.12.132

subject

Has Abstract

pub_date

2014-03-21 00:00:00

pages

717-23

issue

4

eissn

0006-291X

issn

1090-2104

pii

S0006-291X(13)02203-1

journal_volume

445

pub_type

杂志文章

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