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Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation

AuthorsPorta, Josep M. ; Jaillet, Léonard
KeywordsMolecular loop modeling
Energy landscapes
Higher-dimensional continuation
Differential geometry
Issue Date2013
PublisherJohn Wiley & Sons
CitationJournal of Computational Chemistry 34(3): 234-244 (2013)
AbstractThe conformational space of a flexible molecular loop includes the set of conformations fulfilling the geometric loop-closure constraints and its energy landscape can be seen as a scalar field defined on this implicit set. Higher-dimensional continuation tools, recently developed in dynamical systems and also applied to robotics, provide efficient algorithms to trace out implicitly defined sets. This article describes these tools and applies them to obtain full descriptions of the energy landscapes of short molecular loops that, otherwise, can only be partially explored, mainly via sampling. Moreover, to deal with larger loops, this article exploits the higherdimensional continuation tools to find local minima and minimum energy transition paths between them, without deviating from the loop-closure constraints. The proposed techniques are applied to previously studied molecules revealing the intricate structure of their energy landscapes. © 2012 Wiley Periodicals, Inc.
Publisher version (URL)http://dx.doi.org/10.1002/jcc.23128
Identifiersdoi: 10.1002/jcc.23128
issn: 0192-8651
e-issn: 1096-987X
Appears in Collections:(IRII) Artículos
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