EVALUATION OF MOLECULAR DOCKING TOOLS FOR BLIND DOCKING

Eduarda Alves Amaral; Osvaldino Corrêa Da Silveira Júnior; Veridiana Piva Richter; Adriano Werhli; Karina Machado

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Submission

Paper Title

EVALUATION OF MOLECULAR DOCKING TOOLS FOR BLIND DOCKING

Authors

Eduarda Alves Amaral
Osvaldino Corrêa Da Silveira Júnior
Veridiana Piva Richter
Adriano Werhli
Karina Machado

Modality

Poster

Subject area

Proteins and Proteomics

Publishing Date

21/11/2024

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting-2024/837332-evaluation-of-molecular-docking-tools-for-blind-docking

ISBN

978-65-272-0843-3

Keywords

Molecular docking, blind docking, docking tools

Summary

In the search for new drugs, virtual screening is a fundamental tool. It employs computational methods to identify potential drug candidates or bioactive compounds in extensive molecular libraries. An important component of this strategy is the protein-ligand molecular docking, which predicts the best conformation and orientation of a small molecule (ligand) in the binding site of a target receptor. Most docking software consider the three-dimensional structure of proteins and ligands to predict these interactions and often require the indication of the binding site, a region in the target receptor (usually called grid box) where the docking algorithm is going to evaluate the best position and conformation. In many cases the binding site of a target receptor is unknown. To address this challenge, blind docking methods can be employed. Blind docking involves the generation of grid boxes encompassing the entire protein structure, allowing the software to explore potential binding sites without prior information. For this purpose, there are some docking software tools such as QuickVina-W, SwissDock, DockThor, and CB-Dock, among others, which can be used for docking simulations when the binding site of the receptor is unknown. This work proposes to compare different molecular docking tools using blind docking approach and evaluate their efficiency in terms of the accuracy of the prediction of the ligands' experimental position. As input dataset for this evaluation we are considering 10 protein-ligand complexes randomly chosen from the PDBIND2021 database, This input data was prepared using Autodock Tools and Pymol, including the addition of all hydrogens, and charges. The considered tools for evaluation are Vina 2021, QuickVina-W (Qvina-w), SwissDock, CB-Dock and DockThor. Vina and Qvina-w are open-source software that integrates molecular docking calculation and scoring for the best-found positions. SwissDock offers blind docking resources based on fast algorithms and flexible fitting. CB-Dock serves as a widely used docking tool, and the DockThor employs advanced molecular docking techniques. To evaluate the considered tools, we used DockRMSD tool to calculate the Root Mean Square Deviation (RMSD) between the final ligand docked position and the original experimental position. The DockRMSD results confirm that Qvina-w outperformed CB-Dock, Vina and DockThor in terms of accuracy when comparing the average RMSD, suggesting that Qvina-w may be a more interesting choice for blind docking simulations. Regarding formats, all accepted PDB and PDBQT for receptors and MOL2 or PDBQT formats for ligands and if necessary, it is possible to convert the files before docking execution. This study compared different virtual screening tools, highlighting the superior performance of QuickVina-W compared to Vina and the effectiveness of CB-Dock as a quick and efficient option due to being a web tool. Ultimately, these tools offer better flexibility and precision in the search for new medications, contributing significantly to advances in the field of bioinformatics and new drug discovery. As future work we are going to evaluate the blind docking tools for the entire PDBBind 2021.

Title of the Event: 20º Congresso Brasileiro de Bioinformática: X-Meeting 2024
City of the Event: Salvador
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

AMARAL, Eduarda Alves et al.. EVALUATION OF MOLECULAR DOCKING TOOLS FOR BLIND DOCKING.. In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/837332-EVALUATION-OF-MOLECULAR-DOCKING-TOOLS-FOR-BLIND-DOCKING. Access in: 19/05/2025