Property Map Collective Variable as a Useful Tool for a Force Field Correction
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22310%2F22%3A43924445" target="_blank" >RIV/60461373:22310/22:43924445 - isvavai.cz</a>
Alternative codes found
RIV/60461373:22330/22:43924445 RIV/00216224:14610/22:00129035
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.1c00651" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jcim.1c00651</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jcim.1c00651" target="_blank" >10.1021/acs.jcim.1c00651</a>
Alternative languages
Result language
angličtina
Original language name
Property Map Collective Variable as a Useful Tool for a Force Field Correction
Original language description
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/. © 2022 The Authors. Published by American Chemical Society.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Information and Modeling
ISSN
1549-9596
e-ISSN
1549-960X
Volume of the periodical
62
Issue of the periodical within the volume
3
Country of publishing house
US - UNITED STATES
Number of pages
10
Pages from-to
567-576
UT code for WoS article
000762974500013
EID of the result in the Scopus database
2-s2.0-85119603019