Nonlinear vs. linear biasing in Trp-cage folding simulations

J 2015

Nonlinear vs. linear biasing in Trp-cage folding simulations

SPIWOK, Vojtěch, Pavel OBORSKÝ, Jana PAZÚRIKOVÁ, Aleš KŘENEK, Blanka KRÁLOVÁ et. al.

Basic information

Original name

Nonlinear vs. linear biasing in Trp-cage folding simulations

Name in Czech

Vnesení lineárního a nelineárního šumu v simulacích proteinu Trp-cage

Authors

SPIWOK, Vojtěch (203 Czech Republic), Pavel OBORSKÝ (203 Czech Republic), Jana PAZÚRIKOVÁ (703 Slovakia, belonging to the institution), Aleš KŘENEK (203 Czech Republic, belonging to the institution) and Blanka KRÁLOVÁ (203 Czech Republic)

Edition

Journal of the chemical society. Faraday transactions II, Journal of chemical physics, London, Chemical society, 2015, 0021-9606

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 2.894

RIV identification code

RIV/00216224:14610/15:00080979

Organization unit

Institute of Computer Science

DOI

http://dx.doi.org/10.1063/1.4914828

UT WoS

000351530100042

Keywords (in Czech)

molekularni metadynamika; foldovani proteinu

Keywords in English

molecular metadynamics; protein folding

Abstract

V originále

Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

Links

CZ.1.05/3.2.00/08.0144, interní kód MU

Name: CERIT Scientific Cloud (Acronym: CERIT - SC)

Investor: Ministry of Education, Youth and Sports of the CR, 3.2 Promotion and providing information on R&D results

GA15-17269S, research and development project

Name: Simulace komplexních systémů se zesíleným vzorkováním

Investor: Czech Science Foundation

Citovat

SPIWOK, Vojtěch, Pavel OBORSKÝ, Jana PAZÚRIKOVÁ, Aleš KŘENEK and Blanka KRÁLOVÁ. Nonlinear vs. linear biasing in Trp-cage folding simulations. Journal of the chemical society. Faraday transactions II, Journal of chemical physics. London: Chemical society, 2015, vol. 142, No 11, p. nestránkováno, 8 pp. ISSN 0021-9606. Available from: https://dx.doi.org/10.1063/1.4914828.

@article{1309250,
   author = {Spiwok, Vojtěch and Oborský, Pavel and Pazúriková, Jana and Křenek, Aleš and Králová, Blanka},
   article_location = {London},
   article_number = {11},
   doi = {http://dx.doi.org/10.1063/1.4914828},
   keywords = {molecular metadynamics; protein folding},
   language = {eng},
   issn = {0021-9606},
   journal = {Journal of the chemical society. Faraday transactions II, Journal of chemical physics},
   title = {Nonlinear vs. linear biasing in Trp-cage folding simulations},
   url = {http://scitation.aip.org/content/aip/journal/jcp/142/11/10.1063/1.4914828},
   volume = {142},
   year = {2015}
}

TY  - JOUR
ID  - 1309250
AU  - Spiwok, Vojtěch - Oborský, Pavel - Pazúriková, Jana - Křenek, Aleš - Králová, Blanka
PY  - 2015
TI  - Nonlinear vs. linear biasing in Trp-cage folding simulations
JF  - Journal of the chemical society. Faraday transactions II, Journal of chemical physics
VL  - 142
IS  - 11
SP  - nestránkováno
EP  - nestránkováno
PB  - Chemical society
SN  - 00219606
KW  - molecular metadynamics
KW  - protein folding
UR  - http://scitation.aip.org/content/aip/journal/jcp/142/11/10.1063/1.4914828
L2  - http://scitation.aip.org/content/aip/journal/jcp/142/11/10.1063/1.4914828
N2  - Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.
ER  -

SPIWOK, Vojtěch, Pavel OBORSKÝ, Jana PAZÚRIKOVÁ, Aleš KŘENEK and Blanka KRÁLOVÁ. Nonlinear vs. linear biasing in Trp-cage folding simulations. \textit{Journal of the chemical society. Faraday transactions II, Journal of chemical physics}. London: Chemical society, 2015, vol.~142, No~11, p.~nestránkováno, 8 pp. ISSN~0021-9606. Available from: https://dx.doi.org/10.1063/1.4914828.

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