Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F22%3A43924555" target="_blank" >RIV/60461373:22330/22:43924555 - isvavai.cz</a>

Výsledek na webu

<a href="https://journal.r-project.org/articles/RJ-2022-057/" target="_blank" >https://journal.r-project.org/articles/RJ-2022-057/</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.32614/RJ-2022-057" target="_blank" >10.32614/RJ-2022-057</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d

Popis výsledku v původním jazyce

Molecular simulations solve the equation of motion of molecular systems, making the 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have great potential in drug discovery because they can realistically model the structures of protein molecules targeted by drugs, as well as the process of binding of a potential drug to its molecular target. However, routine application of biomolecular simulations is hampered by the very high computational costs of this method. Several methods have been developed to address this problem. One of them, metadynamics, disfavors states of the simulated system that have been already visited and thus forces the system to explore new states. Here we present the package metadynminer and metadynminer3d to analyze and visualize results from metadynamics, in particular those produced by a popular metadynamics package Plumed.

Název v anglickém jazyce

Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d

Popis výsledku anglicky

Molecular simulations solve the equation of motion of molecular systems, making the 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have great potential in drug discovery because they can realistically model the structures of protein molecules targeted by drugs, as well as the process of binding of a potential drug to its molecular target. However, routine application of biomolecular simulations is hampered by the very high computational costs of this method. Several methods have been developed to address this problem. One of them, metadynamics, disfavors states of the simulated system that have been already visited and thus forces the system to explore new states. Here we present the package metadynminer and metadynminer3d to analyze and visualize results from metadynamics, in particular those produced by a popular metadynamics package Plumed.

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

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2022

Kód důvěrnosti údajů

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

Název periodika

R Journal

ISSN

2073-4859

e-ISSN

2073-4859

Svazek periodika

14

Číslo periodika v rámci svazku

3

Stát vydavatele periodika

AT - Rakouská republika

Počet stran výsledku

13

Strana od-do

46-58

Kód UT WoS článku

000925974100005

EID výsledku v databázi Scopus

2-s2.0-85147713977