FRAMEWORKVS 2.0: A FRAMEWORK FOR VIRTUAL SCREENING WITH AUTODOCK VINA

Fabiano Mendonça; Wilgnne Khawan; Paulo Renato Neto; Adriano Werhli; Karina Machado

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Paper Title

FRAMEWORKVS 2.0: A FRAMEWORK FOR VIRTUAL SCREENING WITH AUTODOCK VINA

Authors

Fabiano Mendonça
Wilgnne Khawan
Paulo Renato Neto
Adriano Werhli
Karina Machado

Modality

Software demonstration

Subject area

Database and Software Development

Publishing Date

21/11/2024

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting-2024/837155-frameworkvs-20--a-framework-for-virtual-screening-with-autodock-vina

ISBN

978-65-272-0843-3

Keywords

Virtual screening, Molecular docking, Protein-ligand interactions, Drug discovery, Autodock Vina

Summary

Virtual screening (VS) is a method used in drug discovery to rapidly and effectively identify potential drug candidates from large compound libraries or databases. Rather than testing each compound in a laboratory, virtual screening employs computer algorithms and simulations to predict which compounds are most likely to interact with a specific target protein or biological receptor. This technique enables researchers to prioritize the most promising compounds for further experimental validation and plays a crucial role in the drug discovery process, particularly in the initial stages of identifying lead compounds with potential therapeutic activity, saving time and resources compared to traditional high-throughput laboratory screening methods. For this purpose, the most important step in the Virtual Screening process is typically molecular docking. Protein-ligand molecular docking is the method that predicts the best position, orientation, and conformation of a small molecule (ligand) in the binding site of a target receptor (usually a protein). In this step, there are several softwares capable of performing this simulation, with one of the most commonly used being Autodock Vina. However, this tool can be less intuitive for individuals who are not familiar with the command line. In this context, we propose a new version of FrameworkVS tool to assist in the process of molecular docking simulations .The FrameworkVS operates as a SaaS (Software as a Service) that provides a graphical interface to aid in parameter selection and automate the process of multiple configurations of docking simulations. FrameworkVS 2.0 can consider one target receptor with multiple ligands, when searching for new compounds (VS). In molecular docking, it is still a challenge to incorporate the receptor flexibility and one alternative is to consider multiple protein structures instead of just one. We included this functionality in FrameworkVS 2.0 allowing users to indicate a folder of protein structures (superposed) obtained from Protein Data Bank or generated through molecular dynamics simulations. Additionally, it is possible to vary the coordinates of the binding site to perform multiple simulations with different coordinates, when the binding site is unknown or it is important to evaluate different grid boxes. It is important to mention that the input files can be in different formats: protein in pdb or pdbqt, ligand in mol2 or pdbqt. Thus, after the user configures the experiment in our FrameworkVS 2.0 interface, a Python script is generated and the simulations are conducted locally, using Autodock Vina (versions 1.1-2 or 1.2-3), which needs to be installed beforehand. We have performed simulations with our proposed FrameworkVS, using several different sets of data, varying the number of proteins, the number of ligands and the grid box. This framework shows a promising tool, because it facilitates the molecular docking process through a user-friendly and intuitive interface. As future work we are planning to incorporate multiple scoring functions and to generate versions of the python script to be performed in an distributed computing environment.

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

MENDONÇA, Fabiano et al.. FRAMEWORKVS 2.0: A FRAMEWORK FOR VIRTUAL SCREENING WITH AUTODOCK VINA.. In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/837155-FRAMEWORKVS-20--A-FRAMEWORK-FOR-VIRTUAL-SCREENING-WITH-AUTODOCK-VINA. Access in: 06/05/2025