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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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VSTH: a user-friendly web server for structure-based virtual screening on Tianhe-2.

Qing Mo¹, Zexin Xu¹, Hui Yan¹

¹National Supercomputer Center in Guangzhou, School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou 510006, China.

Bioinformatics (Oxford, England)

|November 17, 2022

Summary

This summary is machine-generated.

The Virtual Screening web server (VSTH) offers a comprehensive workflow for drug discovery. This user-friendly platform facilitates interactive protein preparation, docking site selection, and binding conformer visualization, streamlining virtual screening processes.

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Area of Science:

Computational chemistry
Drug discovery
Bioinformatics

Background:

Virtual screening is a crucial computational method in drug discovery for identifying potential drug candidates.
Existing virtual screening tools often lack comprehensive workflows or user-friendly interfaces.
Efficient preparation of molecular data and analysis of docking results are critical for successful drug design.

Purpose of the Study:

To introduce VSTH, a user-friendly web server designed for the complete virtual screening workflow.
To provide an integrated platform for interactive molecular preparation, docking, and analysis.
To enhance the efficiency and accessibility of virtual screening for researchers.

Main Methods:

Development of a web server integrating customizable visualization tools for molecular preparation and analysis.
Integration of six open-source docking programs for flexible virtual screening computations.
Implementation of filtering and clustering algorithms for analyzing docking conformations based on scores and molecular similarity.

Main Results:

VSTH provides an interactive and user-friendly interface for virtual screening.
The platform supports customizable workflows, including protein preparation, docking site selection, and conformer visualization.
Users can leverage multiple docking programs and personalized parameters for comprehensive screening.
Post-docking analysis includes score-based filtering and cluster analysis for identifying promising drug candidates.

Conclusions:

VSTH offers a complete and accessible solution for virtual screening, empowering researchers in drug discovery.
The integrated workflow and user-friendly design of VSTH streamline the identification of potential therapeutic agents.
The platform's flexibility in docking methods and analysis tools enhances the efficiency of virtual screening campaigns.