Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F25%3A00141536" target="_blank" >RIV/00216224:14310/25:00141536 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00159816:_____/25:00082437 RIV/61989100:27740/25:10258221

Výsledek na webu

<a href="https://jcheminf.biomedcentral.com/articles/10.1186/s13321-025-01005-4" target="_blank" >https://jcheminf.biomedcentral.com/articles/10.1186/s13321-025-01005-4</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13321-025-01005-4" target="_blank" >10.1186/s13321-025-01005-4</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands

Popis výsledku v původním jazyce

Protein-ligand docking is a computational method routinely used in many structural biology applications. It usually involves one receptor and one ligand. The docking of multiple ligands, however, can be important in several situations, such as the study of synergistic effects, substrate and product inhibition, or competitive binding. This can be a challenging and computationally demanding process. By integrating Particle Swarm Optimization into the established AutoDock Vina framework, we provided a powerful tool capable of accelerating drug discovery, and computational enzymology. Here we present Moldina (Multiple-Ligand Molecular Docking over AutoDock Vina), a new algorithm built upon AutoDock Vina. Through comprehensive testing against AutoDock Vina, the algorithm exhibited comparable accuracy in predicting ligand binding conformations while significantly reducing the computational time up to several hundred times. Moldina and the benchmark data are freely available at https://opencode.it4i.eu/permed/moldina-multiple-ligand-molecular-docking-over-autodock-vina and https://github.com/It4innovations/moldina-multiple-ligand-molecular-docking-over-autodock-vina.

Název v anglickém jazyce

Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands

Popis výsledku anglicky

Protein-ligand docking is a computational method routinely used in many structural biology applications. It usually involves one receptor and one ligand. The docking of multiple ligands, however, can be important in several situations, such as the study of synergistic effects, substrate and product inhibition, or competitive binding. This can be a challenging and computationally demanding process. By integrating Particle Swarm Optimization into the established AutoDock Vina framework, we provided a powerful tool capable of accelerating drug discovery, and computational enzymology. Here we present Moldina (Multiple-Ligand Molecular Docking over AutoDock Vina), a new algorithm built upon AutoDock Vina. Through comprehensive testing against AutoDock Vina, the algorithm exhibited comparable accuracy in predicting ligand binding conformations while significantly reducing the computational time up to several hundred times. Moldina and the benchmark data are freely available at https://opencode.it4i.eu/permed/moldina-multiple-ligand-molecular-docking-over-autodock-vina and https://github.com/It4innovations/moldina-multiple-ligand-molecular-docking-over-autodock-vina.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

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

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

2025

Kód důvěrnosti údajů

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

Název periodika

Journal of Cheminformatics

ISSN

1758-2946

e-ISSN

—

Svazek periodika

17

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

10

Strana od-do

1-10

Kód UT WoS článku

001478420800003

EID výsledku v databázi Scopus

2-s2.0-105004187573