Metadynamics in essential coordinates: Free energy simulation of conformational changes

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F07%3A00019130" target="_blank" >RIV/60461373:22330/07:00019130 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Metadynamics in essential coordinates: Free energy simulation of conformational changes

Original language description

We propose an approach that combines an extraction of collective motions of a molecular system with a sampling of its free energy surface. A recently introduced method of metadynamics allows exploration of the free energy surface of a molecular system bymeans of coarse-grained dynamics with flooding of free energy minima. This free energy surface is defined as a function of a set of collective variables (e.g., interatomic distances, angles, torsions, and others). In this study, essential coordinates determined by essential dynamics (principle component analysis) were used as collective variables in metadynamics. First, dynamics of the model system (explicitly solvated alanine dipeptide, Ace-Ala-Nme) was simulated by a classical molecular dynamics simulation. The trajectory (1 ns) was then analyzed by essential dynamics to obtain essential coordinates. The free energy surface as a function of the first and second essential coordinates was then explored by metadynamics. The resulting fr

Czech name

Metadynamika v esenciálních souřadnicích: modelování volných energií konformačních změn

Czech description

Byla provedena metadynamika v esenciálních soužadnicích

Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

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Project

<a href="/en/project/KJB500500512" target="_blank" >KJB500500512: Structural studies of beta-galactosidase from psychrotrophic microorganisms; analysis of biologically and technologically significant complexes</a><br>

Continuities

Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year

2007

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

JOURNAL OF PHYSICAL CHEMISTRY B

ISSN

1520-6106

e-ISSN

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Volume of the periodical

111

Issue of the periodical within the volume

12

Country of publishing house

US - UNITED STATES

Number of pages

4

Pages from-to

3073-3076

UT code for WoS article

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EID of the result in the Scopus database

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