Property Map Collective Variable as a Useful Tool for a Force Field Correction

TRAPL, Dalibor, MArtin KRUPIČKA, Vladimír VIŠŇOVSKÝ, Jana HOZZOVÁ, Jaroslav OĽHA, Aleš KŘENEK a Vojtěch SPIWOK. Property Map Collective Variable as a Useful Tool for a Force Field Correction. Journal of Chemical Information and Modeling. American Chemical Society, 2022, roč. 62, č. 3, s. 567-576. ISSN 1549-9596. Dostupné z: https://dx.doi.org/10.1021/acs.jcim.1c00651.

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

• Originální 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
• WWW: URL
• Impakt faktor: Impact factor: 5.600
• Kód RIV: RIV/00216224:14610/22:00129035
• Organizační jednotka: Ústav výpočetní techniky
• Doi: http://dx.doi.org/10.1021/acs.jcim.1c00651
• UT WoS: 000762974500013
• Klíčová slova anglicky: collective variable; biased potential; force field
• Štítky: rivok
• Příznaky: Mezinárodní význam, Recenzováno

Anotace

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/.

Anotace 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: Název: Zpřesnění molekulárně mechanických potenciálů léčivům podobných molekul metodou property map

Investor: Grantová agentura ČR, Zpřesnění molekulárně mechanických potenciálů léčivům podobných molekul metodou property map