StreaMD: the toolkit for high-throughput molecular dynamics simulations

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F24%3A00601344" target="_blank" >RIV/61388963:_____/24:00601344 - isvavai.cz</a>

Alternative codes found

RIV/61989592:15110/24:73626685

Result on the web

<a href="https://doi.org/10.1186/s13321-024-00918-w" target="_blank" >https://doi.org/10.1186/s13321-024-00918-w</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13321-024-00918-w" target="_blank" >10.1186/s13321-024-00918-w</a>

Result language

angličtina

Original language name

StreaMD: the toolkit for high-throughput molecular dynamics simulations

Original language description

Molecular dynamics simulations serve as a prevalent approach for investigating the dynamic behaviour of proteins and protein-ligand complexes. Due to its versatility and speed, GROMACS stands out as a commonly utilized software platform for executing molecular dynamics simulations. However, its effective utilization requires substantial expertise in configuring, executing, and interpreting molecular dynamics trajectories. Existing automation tools are constrained in their capability to conduct simulations for large sets of compounds with minimal user intervention, or in their ability to distribute simulations across multiple servers. To address these challenges, we developed a Python-based tool that streamlines all phases of molecular dynamics simulations, encompassing preparation, execution, and analysis. This tool minimizes the required knowledge for users engaging in molecular dynamics simulations and can efficiently operate across multiple servers within a network or a cluster. Notably, the tool not only automates trajectory simulation but also facilitates the computation of free binding energies for protein-ligand complexes and generates interaction fingerprints across the trajectory. Our study demonstrated the applicability of this tool on several benchmark datasets. Additionally, we provided recommendations for end-users to effectively utilize the tool. Scientific contribution: The developed tool, StreaMD, is applicable to different systems (proteins, ligands and their complexes including co-factors) and requires a little user knowledge to setup and run molecular dynamics simulations. Other features of StreaMD are seamless integration with calculation of MM-GBSA/PBSA binding free energies and protein-ligand interaction fingerprints, and running of simulations within distributed environments. All these will facilitate routine and massive molecular dynamics simulations.

Czech name

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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

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

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

2024

Confidentiality

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

Name of the periodical

Journal of Cheminformatics

ISSN

1758-2946

e-ISSN

1758-2946

Volume of the periodical

16

Issue of the periodical within the volume

1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

13

Pages from-to

123

UT code for WoS article

001352018500001

EID of the result in the Scopus database

2-s2.0-85208734084