Analysis of metadynamics simulations by metadynminer.py

J 2024

Analysis of metadynamics simulations by metadynminer.py

BERANEK, Jan; Aleš KŘENEK a Vojtěch SPIWOK

Základní údaje

Originální název

Analysis of metadynamics simulations by metadynminer.py

Autoři

BERANEK, Jan; Aleš KŘENEK (203 Česká republika, domácí) a Vojtěch SPIWOK (203 Česká republika)

Vydání

Bioinformatics, OXFORD, Oxford University Press, 2024, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.400 v roce 2023

Kód RIV

RIV/00216224:14610/24:00137666

Organizační jednotka

Ústav výpočetní techniky

DOI

http://dx.doi.org/10.1093/bioinformatics/btae614

UT WoS

001343040600001

EID Scopus

2-s2.0-85207984430

Klíčová slova anglicky

metadynamics; biomolecular simulation; web application

Štítky

rivok

Změněno: 4. 4. 2025 13:13, Mgr. Eva Špillingová

Anotace

V originále

Motivation: Molecular dynamics simulation is very useful but computationally demanding method of studying dynamics of biomolecular systems. Many enhanced sampling methods were developed in order to obtain the desired results in available computational time. Metadynamics and its variants are common enhanced sampling methods used for this purpose. Metadynamics simulations allow the user to gather large amounts of data, which have to be analyzed to elucidate the properties of the studied system. Results: Here, we present metadynminer.py, a Python package that allows easy and user-friendly analysis and visualization of the results obtained from metadynamics simulations. The built-in functions automate frequent tasks and make the package easy to use for new users, while its many customization options and object-oriented nature allow for integration into specialized data analysis workflows by more advanced users.

Návaznosti

GA22-29667S, projekt VaV

Název: Analýza a vzorkování molekulárních simulací pomocí kontradiktorních autokodérů

Investor: Grantová agentura ČR, Analýza a vzorkování molekulárních simulací pomocí kontradiktorních autokodérů

LM2023055, projekt VaV

Název: Česká národní infrastruktura pro biologická data

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, ELIXIR-CZ: Česká národní infrastruktura pro biologická data

90254, velká výzkumná infrastruktura

Název: e-INFRA CZ II

Citovat

BERANEK, Jan; Aleš KŘENEK a Vojtěch SPIWOK. Analysis of metadynamics simulations by metadynminer.py. Bioinformatics. OXFORD: Oxford University Press, 2024, roč. 40, č. 10, s. 1-4. ISSN 1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btae614.

@article{2452397,
   author = {Beranek, Jan and Křenek, Aleš and Spiwok, Vojtěch},
   article_location = {OXFORD},
   article_number = {10},
   doi = {http://dx.doi.org/10.1093/bioinformatics/btae614},
   keywords = {metadynamics; biomolecular simulation; web application},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {Analysis of metadynamics simulations by metadynminer.py},
   url = {https://doi.org/10.1093/bioinformatics/btae614},
   volume = {40},
   year = {2024}
}

TY  - JOUR
ID  - 2452397
AU  - Beranek, Jan - Křenek, Aleš - Spiwok, Vojtěch
PY  - 2024
TI  - Analysis of metadynamics simulations by metadynminer.py
JF  - Bioinformatics
VL  - 40
IS  - 10
SP  - 1-4
EP  - 1-4
PB  - Oxford University Press
SN  - 13674803
KW  - metadynamics
KW  - biomolecular simulation
KW  - web application
UR  - https://doi.org/10.1093/bioinformatics/btae614
N2  - Motivation: Molecular dynamics simulation is very useful but computationally demanding method of studying dynamics of biomolecular systems. Many enhanced sampling methods were developed in order to obtain the desired results in available computational time. Metadynamics and its variants are common enhanced sampling methods used for this purpose. Metadynamics simulations allow the user to gather large amounts of data, which have to be analyzed to elucidate the properties of the studied system. Results: Here, we present metadynminer.py, a Python package that allows easy and user-friendly analysis and visualization of the results obtained from metadynamics simulations. The built-in functions automate frequent tasks and make the package easy to use for new users, while its many customization options and object-oriented nature allow for integration into specialized data analysis workflows by more advanced users.
ER  -

BERANEK, Jan; Aleš KŘENEK a Vojtěch SPIWOK. Analysis of metadynamics simulations by metadynminer.py. \textit{Bioinformatics}. OXFORD: Oxford University Press, 2024, roč.~40, č.~10, s.~1-4. ISSN~1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btae614.

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