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J Chem Inf Model. 2013 May 24;53(5):1235-52. doi: 10.1021/ci4000294. Epub 2013 May 16.

TRAPP: a tool for analysis of transient binding pockets in proteins.

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1
Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. daria.kokh@h-its.org

Abstract

We present TRAPP (TRAnsient Pockets in Proteins), a new automated software platform for tracking, analysis, and visualization of binding pocket variations along a protein motion trajectory or within an ensemble of protein structures that may encompass conformational changes ranging from local side chain fluctuations to global backbone motions. TRAPP performs accurate grid-based calculations of the shape and physicochemical characteristics of a binding pocket for each structure and detects the conserved and transient regions of the pocket in an ensemble of protein conformations. It also provides tools for tracing the opening of a particular subpocket and residues that contribute to the binding site. TRAPP thus enables an assessment of the druggability of a disease-related target protein taking its flexibility into account.

PMID:
23621586
DOI:
10.1021/ci4000294
[Indexed for MEDLINE]
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