KVFinder-web: a web-based application for detecting and characterizing biomolecular cavities.

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Molecular interactions crucial for catalysis often occur in cavities on biomolecular surfaces.
• These interactions depend on geometric and physicochemical complementarity between small molecules and their receptors.
• Understanding these binding sites is key to drug discovery and understanding biological mechanisms.

Purpose of the Study:

• To introduce KVFinder-web, an open-source, web-based application for cavity detection and characterization in biomolecular structures.
• To provide researchers with an accessible tool for analyzing potential molecular interaction sites.

Main Methods:

• KVFinder-web integrates the parKVFinder software into a dual-component system: a RESTful web service and a graphical web portal.
• The web service manages job requests, performs cavity detection, and characterization.
• The web portal allows users to customize parameters, submit jobs, and visualize results.

Main Results:

• A publicly accessible KVFinder-web application is available at https://kvfinder-web.cnpem.br.
• The application runs on cloud infrastructure using Docker containers, ensuring scalability and ease of deployment.
• Users can utilize the public service or deploy KVFinder-web locally for customized analysis.

Conclusions:

• KVFinder-web offers a valuable, user-friendly platform for biomolecular cavity analysis.
• Its flexible deployment options cater to diverse research needs, from quick analyses to customized local setups.
• This tool facilitates the study of molecular interactions and aids in the identification of potential drug targets.