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Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d

The result's identifiers

  • Result code in 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>

  • Result on the web

    <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>

Alternative languages

  • Result language

    angličtina

  • Original language name

    Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d

  • Original language description

    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.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • 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

    R Journal

  • ISSN

    2073-4859

  • e-ISSN

    2073-4859

  • Volume of the periodical

    14

  • Issue of the periodical within the volume

    3

  • Country of publishing house

    AT - AUSTRIA

  • Number of pages

    13

  • Pages from-to

    46-58

  • UT code for WoS article

    000925974100005

  • EID of the result in the Scopus database

    2-s2.0-85147713977