PocketAnnotate statistics

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PocketAnnotate specifications

Information


Unique identifier OMICS_13738
Name PocketAnnotate
Interface Web user interface
Restrictions to use None
Input data An apo protein structure, PDB code of protein bound with a ligand, an own sub-structure (any zone of continuous/discontinuous residues in structure) for comparison.
Input format PDB
Output data The results produced by all three algorithms are displayed on separate html pages during the pipeline. PocketDepth predicts the putative binding sites, PocketMatch results are displayed in a scroll bar along with the scores in a separate html page, PocketAlign results are displayed in a separate interactive window, with both the selected sites superposed and report the correspondences between the residues in the pair aligned with RMSD scores.
Computer skills Basic
Stability Stable
Requirements
Java
Maintained No

Documentation


Maintainer


This tool is not available anymore.

Publication for PocketAnnotate

PocketAnnotate in publication

PMCID: 5376175
PMID: 25220818
DOI: 10.1038/srep06356

[…] out. in 2442 of 3209 complexes, a pocket at a similar location as well as the same ligand association is predicted. the entire site-based function annotation pipeline has also been validated in pocketannotate using apo-holo protein datasets. put together, it is clear that methods used for binding site identification, measuring similarities between binding sites and obtaining ligand […]


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PocketAnnotate institution(s)
Department of Biochemistry, Indian Institute of Science, Bangalore, India
PocketAnnotate funding source(s)
This work was supported by Department of Biotechnology (DBT); Government of India.

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