Efficient Estimation of Absolute Binding Free Energy for a Homeodomain-DNA Complex from Nonequilibrium Pulling Simulations

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F20%3A00524101" target="_blank" >RIV/61388963:_____/20:00524101 - isvavai.cz</a>

Alternative codes found

RIV/00216208:11310/20:10422518

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.0c00006" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jctc.0c00006</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jctc.0c00006" target="_blank" >10.1021/acs.jctc.0c00006</a>

Result language

angličtina

Original language name

Efficient Estimation of Absolute Binding Free Energy for a Homeodomain-DNA Complex from Nonequilibrium Pulling Simulations

Original language description

Estimation of binding free energies is one of the central aims of simulations of biomolecular complexes. We explore the accuracy and efficiency of setups based on nonequilibrium pulling simulations applied to the estimation of binding affinities of DNA-binding proteins. Absolute binding free energies are calculated over a range of temperatures and compared to results obtained previously using an equilibrium method. We show that realistic binding affinities can be obtained with the presented nonequilibrium approach, which also entails lower computational requirements. Errors of the binding free energy estimates are investigated and are shown to be comparable to those observed previously. Bounds are provided on the convergence of the errors with respect to the number of pulling simulations performed and with respect to the applied pull rate.

Czech name

—

Czech description

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Type

J_imp - 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

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2020

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Volume of the periodical

16

Issue of the periodical within the volume

4

Country of publishing house

US - UNITED STATES

Number of pages

8

Pages from-to

2034-2041

UT code for WoS article

000526313000004

EID of the result in the Scopus database

2-s2.0-85083545114