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- Title
tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules.
- Authors
SEELIGER, DANIEL; DE GROOT, BERT L.
- Abstract
Conformational flexibility of bioactive molecules poses a major challenge to computational biology. tCONCOORD generates structure ensembles based on geometrical considerations and has been successfully applied to predict protein conformational flexibility and essential degrees of freedom. We have now developed a graphical user interface (GUI) for tCONCOORD, which substantially facilitates the simulation setup and provides valuable insights into the structure analysis and constraint definition process in tCONCOORD. Moreover, users can influence the constraint definition process by interactively turning interactions on and off, defining completely rigid or flexible regions, or by applying artifical constraints that cause a biased sampling of the conformational space. This interface offers a versatile environment not only for the setup and analysis of tCONCOORD simulations, but also for molecular modeling and structure analysis in general. Both tCONCOORD<NOTER>*</NOTER> and the tCONCOORD-GUI<NOTER>†</NOTER> are distributed freely. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
- Subjects
MOLECULES; COMPUTATIONAL biology; GEOMETRY; GRAPHICAL user interfaces; COMPUTER systems
- Publication
Journal of Computational Chemistry, 2009, Vol 30, Issue 7, p1160
- ISSN
0192-8651
- Publication type
Article
- DOI
10.1002/jcc.21127