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TRAPP: a tool for analysis of Transient binding Pockets in Proteins

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 c...

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Bibliographic Details
Main Authors: Kokh, Daria B. (Author) , Richter, Stefan (Author) , Henrich, Stefan (Author) , Czodrowski, Paul (Author) , Rippmann, Friedrich (Author) , Wade, Rebecca C. (Author)
Format: Article (Journal)
Language:English
Published: April 27, 2013
In: Journal of chemical information and modeling
Year: 2013, Volume: 53, Issue: 5, Pages: 1235-1252
ISSN:1549-960X
DOI:10.1021/ci4000294
Online Access:Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1021/ci4000294
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Author Notes:Daria B. Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann, and Rebecca C. Wade
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Summary: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.
Item Description:Gesehen am 25.03.2021
Physical Description:Online Resource
ISSN:1549-960X
DOI:10.1021/ci4000294

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