From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library

Area of Science:

• Computational biology
• Structural bioinformatics
• Cheminformatics

Background:

• Computational approaches are crucial for modern life science research, assisting with data analysis, interpretation, and visualization.
• Simulation methods predict physicochemical properties and aid in understanding complex macromolecular phenomena.

Purpose of the Study:

• To provide an overview of computational methods developed to support researchers across all life science disciplines.
• To introduce user-friendly software solutions for common bioinformatics and cheminformatics challenges.

Main Methods:

• Development of an all-in-one web service platform, ProteinsPlus, integrating various prediction and analysis tools.
• Creation of a software package offering tools for cheminformatics tasks (e.g., file conversion, virtual screening) and structural bioinformatics (e.g., inverse screening, pattern searching).

Main Results:

• ProteinsPlus offers solutions for pocket and druggability prediction, hydrogen placement, structure quality assessment, ensemble generation, protein-protein interaction classification, and 2D-interaction visualization.
• The software package facilitates cheminformatics tasks like file format conversion, dataset processing, SMARTS editing, fragment enumeration, and ligand-based virtual screening.
• Structural bioinformatics tools include inverse screening, binding site alignment, and interaction pattern searching across structure libraries.

Conclusions:

• The developed software and web platform provide comprehensive computational support for life science researchers.
• These tools aim to streamline research workflows, from data analysis to prediction and discovery, leveraging state-of-the-art bioinformatics and cheminformatics approaches.