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

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/00216208:11310/20:10422518

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2020

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Theory and Computation

ISSN

1549-9618

e-ISSN

—

Svazek periodika

16

Číslo periodika v rámci svazku

4

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

8

Strana od-do

2034-2041

Kód UT WoS článku

000526313000004

EID výsledku v databázi Scopus

2-s2.0-85083545114