Detailed Information on Publication Record
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.Basic information
Original name
Property Map Collective Variable as a Useful Tool for a Force Field Correction
Name in Czech
Property Map Collective Variable as a Useful Tool for a Force Field Correction
Authors
TRAPL, Dalibor (203 Czech Republic), MArtin KRUPIČKA (203 Czech Republic), Vladimír VIŠŇOVSKÝ (703 Slovakia, belonging to the institution), Jana HOZZOVÁ (703 Slovakia, belonging to the institution), Jaroslav OĽHA (703 Slovakia, belonging to the institution), Aleš KŘENEK (203 Czech Republic, guarantor, belonging to the institution) and Vojtěch SPIWOK (203 Czech Republic)
Edition
Journal of Chemical Information and Modeling, American Chemical Society, 2022, 1549-9596
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Impact factor
Impact factor: 5.600
RIV identification code
RIV/00216224:14610/22:00129035
Organization unit
Institute of Computer Science
UT WoS
000762974500013
Keywords in English
collective variable; biased potential; force field
Tags
Tags
International impact, Reviewed
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/.
In Czech
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/.
Links
| GA19-16857S, research and development project |
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