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Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding
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SYSNO ASEP 0369244 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding Author(s) Vymětal, Jiří (UOCHB-X) RID, ORCID
Vondrášek, Jiří (UOCHB-X) RID, ORCIDNumber of authors 2 Source Title Journal of Physical Chemistry A. - : American Chemical Society - ISSN 1089-5639
Roč. 115, č. 41 (2011), s. 11455-11465Number of pages 11 s. Language eng - English Country US - United States Keywords metadynamics ; protein folding ; molecular simulations ; collective coordinates Subject RIV CF - Physical ; Theoretical Chemistry CEZ AV0Z40550506 - UOCHB-X (2005-2011) UT WOS 000295700600037 DOI 10.1021/jp2065612 Annotation 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Year of Publishing 2012
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