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.

Základní údaje

Originální název

Nonlinear vs. linear biasing in Trp-cage folding simulations

Název česky

Vnesení lineárního a nelineárního šumu v simulacích proteinu Trp-cage

Autoři

SPIWOK, Vojtěch (203 Česká republika), Pavel OBORSKÝ (203 Česká republika), Jana PAZÚRIKOVÁ (703 Slovensko, domácí), Aleš KŘENEK (203 Česká republika, domácí) a Blanka KRÁLOVÁ (203 Česká republika)

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.894

Kód RIV

RIV/00216224:14610/15:00080979

Organizační jednotka

Ústav výpočetní techniky

DOI

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

UT WoS

000351530100042

Klíčová slova česky

molekularni metadynamika; foldovani proteinu

Klíčová slova anglicky

molecular metadynamics; protein folding

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 27. 4. 2018 10:31, Mgr. Alena Mokrá

Anotace

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.

Návaznosti

CZ.1.05/3.2.00/08.0144, interní kód MU

Název: CERIT Scientific Cloud (Akronym: CERIT - SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud, 3.2 Propagace a informovanost

GA15-17269S, projekt VaV

Název: Simulace komplexních systémů se zesíleným vzorkováním

Investor: Grantová agentura ČR, Simulace komplexních systémů se zesíleným vzorkováním

Citovat

SPIWOK, Vojtěch, Pavel OBORSKÝ, Jana PAZÚRIKOVÁ, Aleš KŘENEK a 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, roč. 142, č. 11, s. nestránkováno, 8 s. ISSN 0021-9606. Dostupné z: 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 a 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, roč.~142, č.~11, s.~nestránkováno, 8 s. ISSN~0021-9606. Dostupné z: https://dx.doi.org/10.1063/1.4914828.

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