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SplitPocket specifications

Information


Unique identifier OMICS_04693
Name SplitPocket
Interface Web user interface
Restrictions to use None
Input data The coordinates of a structure.
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Wen-Hsiung Li

Publication for SplitPocket

SplitPocket citations

 (3)
library_books

Computational Analysis of Gynura bicolor Bioactive Compounds as Dipeptidyl Peptidase IV Inhibitor

2017
Adv Bioinformatics
PMCID: 5591938
PMID: 28932239
DOI: 10.1155/2017/5124165

[…] determinant of substrate specificity. The selection of the largest binding pocket of DPPIV receptor PDB ID: 4A5S for ligand docking was supported by the physicochemical features of the pocket itself. SplitPocket analysis had identified the presence of a split pocket which is detectable when a functional pocket binds to a ligand, substrate, or other proteins or peptides causing the interaction betw […]

library_books

Molecular Basis of ABHD5 Lipolysis Activation

2017
Sci Rep
PMCID: 5314347
PMID: 28211464
DOI: 10.1038/srep42589

[…] a refined model using the weighted Delaunay triangulation. We then identified putative pockets (local surfaces) of structural models by applying the flow algorithm (http://cast.engr.uic.edu/) and the SplitPocket algorithm (http://pocket.med.wayne.edu/) to characterize local protein surfaces. For each identified pocket, we computed geometric measurements for pocket residues, solvent accessible area […]

library_books

Building a virtual ligand screening pipeline using free software: a survey

2015
Brief Bioinform
PMCID: 4793892
PMID: 26094053
DOI: 10.1093/bib/bbv037

[…] . Should the binding site not be known from previous crystallized protein–ligand complexes, several binding pocket prediction methods are available, e.g. MetaPocket [], DoGSiteScorer [], CASTp [] and SplitPocket [] (see [] for a review of related approaches). Next, a quality control is necessary, as protein crystal structures in public repositories like the PDB often contain errors or missing resi […]

Citations

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SplitPocket institution(s)
Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA; Center for Computational Biology and Bioinformatics, University of Texas at Austin, One University Station, Austin, TX, USA; Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
SplitPocket funding source(s)
Supported by National Institutes of Health (grant GM30998); Academia Sinica, Taiwan.

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