Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands
Radek Halfar1, Jiří Damborský2,3, Sérgio M Marques4,5
1IT4Innovations, VSB - Technical University of Ostrava, 70800, Ostrava, Czech Republic. radek.halfar@vsb.cz.
Journal of Cheminformatics
|April 28, 2025
Summary
Moldina is a new computational tool that accelerates drug discovery by efficiently performing multiple-ligand molecular docking. This algorithm significantly reduces computation time while maintaining accuracy in predicting ligand binding, aiding structural biology and drug development.
Area of Science:
- Computational chemistry
- Structural biology
- Drug discovery
Background:
- Protein-ligand docking is crucial for structural biology, typically analyzing one receptor and one ligand.
- Docking multiple ligands is vital for studying synergistic effects, inhibition, and competitive binding, but it is computationally intensive.
Purpose of the Study:
- To introduce Moldina, a novel algorithm for multiple-ligand molecular docking.
- To enhance the efficiency and speed of computational drug discovery and enzymology.
Main Methods:
- Integration of Particle Swarm Optimization with the AutoDock Vina framework.
- Development of the Moldina (Multiple-Ligand Molecular Docking over AutoDock Vina) algorithm.
- Comprehensive benchmarking against the established AutoDock Vina.
Main Results:
- Moldina demonstrates comparable accuracy to AutoDock Vina in predicting ligand binding conformations.
- The algorithm achieves significant reductions in computational time, up to several hundredfold.
- Moldina offers a powerful and accelerated approach to multiple-ligand docking.
Conclusions:
- Moldina provides a computationally efficient solution for multiple-ligand molecular docking.
- The tool accelerates drug discovery and computational enzymology applications.
- Moldina is freely available for research and development.
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