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<p>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 <a href="https://opencode.it4i.eu/permed/moldina-multiple-ligand-molecular-docking-over-autodock-vina">https://opencode.it4i.eu/permed/moldina-multiple-ligand-molecular-docking-over-autodock-vina</a> and <a href="https://github.com/It4innovations/moldina-multiple-ligand-molecular-docking-over-autodock-vina">https://github.com/It4innovations/moldina-multiple-ligand-molecular-docking-over-autodock-vina</a>.</p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年4月28日

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  • Radek Halfar,
  • Jiří Damborský,
  • Sérgio M. Marques,
  • Jan Martinovič

摘要

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.