SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking.

Area of Science:

• Computational chemistry
• Drug discovery
• Bioinformatics

Background:

• * *In silico* assessment of protein-ligand interactions is crucial in modern drug discovery.
• * Existing tools often require specialized knowledge and software installation.

Purpose of the Study:

• * To introduce SeamDock, a web server simplifying small molecule docking for nonspecialists and students.
• * To provide an integrated platform for global, local, and hierarchical docking approaches.
• * To enhance user experience through interactive 3D visualization and seamless online collaboration.

Main Methods:

• * Integration of multiple docking tools within a unified web framework.
• * Implementation of a Seamless framework for interactive browser-based navigation.
• * Development of advanced 3D visualization for ligands, receptors, and docking poses.
• * Facilitation of collaborative docking sessions and visualization states.

Main Results:

• * SeamDock provides an accessible online service requiring only a web browser.
• * The platform supports global and local docking, with a hierarchical approach for site identification.
• * Interactive 3D visualization and collaborative features enhance usability.
• * The service is free, didactic, and suitable for education and training.

Conclusions:

• * SeamDock democratizes *in silico* drug discovery by lowering the technical barrier.
• * It serves as a valuable educational resource for teaching molecular docking and drug design principles.
• * The platform's evolving nature promises continuous improvement and expanded functionality.