PEP-SiteFinder statistics

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PEP-SiteFinder specifications

Information


Unique identifier OMICS_05697
Name PEP-SiteFinder
Interface Web user interface
Restrictions to use None
Input data The structure of the protein in interaction with the peptide and the amino acid sequence of the peptide interacting with the protein.
Input format PDB, FASTA
Output data An interactive page allowing to browse the 3D structure of the best complexes generated, files corresponding to the protein with the interaction propensities set in the temperature factor field and to the peptide poses, with a PyMOL script to drive and file listing the propensities per residue.
Output format PDB
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pierre Tufféry <>

Publication for PEP-SiteFinder

PEP-SiteFinder in publications

 (2)
PMCID: 5570166
PMID: 28460116
DOI: 10.1093/nar/gkx335

[…] interface propensity are predicted as ‘interface’, where n is the number of residues that makes at least one contact in the model structure of the complex. interface predictions using pepsite () and pep-sitefinder () were made using their respective web servers. for pep-sitefinder, the top n residues were selected in the same way (except for 2jam, for which prediction failed). for pepsite, […]

PMCID: 5238551
PMID: 28144341
DOI: 10.3762/bjoc.12.267

[…] probes in identifying hot spots in structures and was more recently extended to include any user provided small molecule as an additional probe [–]. many other binding pocket finding programs exist. pep-sitefinder [], sitemap available through schrodinger [] and molsite [] are a few of these programs., when the binding pocket of a target is known one significant characteristic to be calculated […]


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PEP-SiteFinder institution(s)
INSERM U973, MTi, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Ressource Parisienne en Bioinformatique Structurale, Paris, France; Technische Universität München, München, Germany
PEP-SiteFinder funding source(s)
Supported by French IA bioinformatics BipBip grant; INSERM UMR-S and Ressource Parisienne en Bioinformatique Structurale.

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