Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding

0369244 - ÚOCHB 2012 RIV US eng J - Článek v odborném periodiku
Vymětal, Jiří - Vondrášek, Jiří
Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding.
Journal of Physical Chemistry A. Roč. 115, č. 41 (2011), s. 11455-11465. ISSN 1089-5639. E-ISSN 1520-5215
Výzkumný záměr: CEZ:AV0Z40550506
Klíčová slova: metadynamics * protein folding * molecular simulations * collective coordinates
Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
Impakt faktor: 2.946, rok: 2011

Effective simulations of proteins, their complexes, and other amino acid polymers such as peptides or peptoids are critically dependent on the performance of the simulation methods and their ability to map the conformational space of the molecule in question. In the presented study, we show that metadynamics and chosen collective coordinates-the principal moments of the tensors of gyration and inertia, the principal radii of gyration around the principal axes, asphericity, acylindricity, and anisotropy-can be used as a powerful combination to map the conformational space of peptides and proteins.
Trvalý link: http://hdl.handle.net/11104/0006737