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...
Gespeichert in:
| Hauptverfasser: | , , , , , |
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| Dokumenttyp: | Article (Journal) |
| Sprache: | Englisch |
| Veröffentlicht: |
April 27, 2013
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| In: |
Journal of chemical information and modeling
Year: 2013, Jahrgang: 53, Heft: 5, Pages: 1235-1252 |
| ISSN: | 1549-960X |
| DOI: | 10.1021/ci4000294 |
| Online-Zugang: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1021/ci4000294
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| Verfasserangaben: | Daria B. Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann, and Rebecca C. Wade |
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| 520 | |a 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. | ||
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