TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins
- Publikationstyp:
- Zeitschriftenaufsatz
- Metadaten:
-
- Autoren
- Dania B Kokh
- Stefan Richter
- Stefan Henrich
- Paul Czodrowski
- Friedrich Rippmann
- Rebecca C Wade
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000319650800021&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1021/ci4000294
- eISSN
- 1549-960X
- Externe Identifier
- Clarivate Analytics Document Solution ID: 154DD
- PubMed Identifier: 23621586
- ISSN
- 1549-9596
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- JOURNAL OF CHEMICAL INFORMATION AND MODELING
- Paginierung
- 1235 - 1252
- Datum der Veröffentlichung
- 2013
- Status
- Published
- Titel
- TRAPP: A Tool for Analysis of <i>Tra</i>nsient Binding <i>P</i>ockets in <i>P</i>roteins
- Sub types
- Article
- Ausgabe der Zeitschrift
- 53
Datenquelle: Web of Science (Lite)
- Andere Metadatenquellen:
-
- Autoren
- Daria B Kokh
- Stefan Richter
- Stefan Henrich
- Paul Czodrowski
- Friedrich Rippmann
- Rebecca C Wade
- DOI
- 10.1021/ci4000294
- eISSN
- 1549-960X
- ISSN
- 1549-9596
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- Journal of Chemical Information and Modeling
- Sprache
- en
- Online publication date
- 2013
- Paginierung
- 1235 - 1252
- Datum der Veröffentlichung
- 2013
- Status
- Published
- Herausgeber
- American Chemical Society (ACS)
- Herausgeber URL
- http://dx.doi.org/10.1021/ci4000294
- Datum der Datenerfassung
- 2024
- Titel
- TRAPP: A Tool for Analysis of<i>Tra</i>nsient Binding<i>P</i>ockets in<i>P</i>roteins
- Ausgabe der Zeitschrift
- 53
Datenquelle: Crossref
- 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.
- Addresses
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. daria.kokh@h-its.org
- Autoren
- Daria B Kokh
- Stefan Richter
- Stefan Henrich
- Paul Czodrowski
- Friedrich Rippmann
- Rebecca C Wade
- DOI
- 10.1021/ci4000294
- eISSN
- 1549-960X
- Externe Identifier
- PubMed Identifier: 23621586
- Open access
- false
- ISSN
- 1549-9596
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- Journal of chemical information and modeling
- Schlüsselwörter
- Proteins
- Ligands
- Computational Biology
- Binding Sites
- Principal Component Analysis
- Software
- Molecular Dynamics Simulation
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2013
- Paginierung
- 1235 - 1252
- Datum der Veröffentlichung
- 2013
- Status
- Published
- Datum der Datenerfassung
- 2013
- Titel
- TRAPP: a tool for analysis of transient binding pockets in proteins.
- Sub types
- Research Support, Non-U.S. Gov't
- Journal Article
- Ausgabe der Zeitschrift
- 53
Datenquelle: Europe PubMed Central
- 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.
- Autoren
- Daria B Kokh
- Stefan Richter
- Stefan Henrich
- Paul Czodrowski
- Friedrich Rippmann
- Rebecca C Wade
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/23621586
- DOI
- 10.1021/ci4000294
- eISSN
- 1549-960X
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- J Chem Inf Model
- Schlüsselwörter
- Binding Sites
- Computational Biology
- Ligands
- Molecular Dynamics Simulation
- Principal Component Analysis
- Proteins
- Software
- Sprache
- eng
- Country
- United States
- Paginierung
- 1235 - 1252
- Datum der Veröffentlichung
- 2013
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2013
- Titel
- TRAPP: a tool for analysis of transient binding pockets in proteins.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 53
Datenquelle: PubMed
- Beziehungen:
-