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

Result code in 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>
Alternative codes found
RIV/00159816:_____/25:00082437 RIV/61989100:27740/25:10258221
Result on the web
<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>

Result language
angličtina
Original language name
Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands
Original language description
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.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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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
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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