2022
Property Map Collective Variable as a Useful Tool for a Force Field Correction
TRAPL, Dalibor, MArtin KRUPIČKA, Vladimír VIŠŇOVSKÝ, Jana HOZZOVÁ, Jaroslav OĽHA et. al.Základní údaje
Originální název
Property Map Collective Variable as a Useful Tool for a Force Field Correction
Název česky
Property Map Collective Variable as a Useful Tool for a Force Field Correction
Autoři
TRAPL, Dalibor (203 Česká republika), MArtin KRUPIČKA (203 Česká republika), Vladimír VIŠŇOVSKÝ (703 Slovensko, domácí), Jana HOZZOVÁ (703 Slovensko, domácí), Jaroslav OĽHA (703 Slovensko, domácí), Aleš KŘENEK (203 Česká republika, garant, domácí) a Vojtěch SPIWOK (203 Česká republika)
Vydání
Journal of Chemical Information and Modeling, American Chemical Society, 2022, 1549-9596
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10201 Computer sciences, information science, bioinformatics
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Odkazy
Impakt faktor
Impact factor: 5.600
Kód RIV
RIV/00216224:14610/22:00129035
Organizační jednotka
Ústav výpočetní techniky
UT WoS
000762974500013
Klíčová slova anglicky
collective variable; biased potential; force field
Štítky
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 14. 3. 2023 15:51, Mgr. Alena Mokrá
V originále
The accuracy of biomolecular simulations depends on the accuracy of an empirical molecular mechanics potential known as a force field: a set of parameters and expressions to estimate the potential from atomic coordinates. Accurate parametrization of force fields for small organic molecules is a challenge due to their high diversity. One of the possible approaches is to apply a correction to the existing force fields. Here, we propose an approach to estimate the density functional theory (DFT)-derived force field correction which is calculated during the run of molecular dynamics without significantly affecting its speed. Using the formula known as a property map collective variable, we approximate the force field correction by a weighted average of this force field correction calculated only for a small series of reference structures. To validate this method, we used seven AMBER force fields, and we show how it is possible to convert one force field to behave like the other one. We also present the force field correction for the important anticancer drug Imatinib as a use case example. Our method appears to be suitable for adjusting the force field for general drug-like molecules. We provide a pipeline that generates the correction; this pipeline is available at https://pmcvff-correction.cerit-sc.cz/.
Česky
The accuracy of biomolecular simulations depends on the accuracy of an empirical molecular mechanics potential known as a force field: a set of parameters and expressions to estimate the potential from atomic coordinates. Accurate parametrization of force fields for small organic molecules is a challenge due to their high diversity. One of the possible approaches is to apply a correction to the existing force fields. Here, we propose an approach to estimate the density functional theory (DFT)-derived force field correction which is calculated during the run of molecular dynamics without significantly affecting its speed. Using the formula known as a property map collective variable, we approximate the force field correction by a weighted average of this force field correction calculated only for a small series of reference structures. To validate this method, we used seven AMBER force fields, and we show how it is possible to convert one force field to behave like the other one. We also present the force field correction for the important anticancer drug Imatinib as a use case example. Our method appears to be suitable for adjusting the force field for general drug-like molecules. We provide a pipeline that generates the correction; this pipeline is available at https://pmcvff-correction.cerit-sc.cz/.
Návaznosti
| GA19-16857S, projekt VaV |
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