VidockS: A Spatially-Inspired, Open-Source Platform for Molecular Docking and Future Molecular Dynamics

Molecular docking is a cornerstone of structure-based drug design (SBDD), enabling prediction of small-molecule binding modes and affinities to protein targets. Yet adoption remains hindered by command-line complexity, fragmented toolchains, and privacy concerns when submitting proprietary compound structures to third-party servers. We present VidockS, a free,open-source, browser-based platform that removes every one of these barriers. Currently powered by AutoDock Vina, VidockS features client-side cheminformatics via RDKit.js (WebAssembly), real-time 3D visualization with 3Dmol.js, and a spatially-inspired interface designed for intuitive SBDD workflows. To ensure absolute user privacy, VidockS stores no user data server-side; all session history is cached entirely in the user's own browser via IndexedDB. We validate VidockS across three well-characterised pharmacological systems: Aspirin/COX-1 (PDB: 3HTB, -6.5 kcal/mol), Caffeine/Adenosine Deaminase (PDB: 4HJ0, -6.1 kcal/mol), and Ibuprofen/COX-2 (PDB: 2HYY, -8.4 kcal/mol), all consistent with published literature values and each completed in under 30 seconds on a consumer laptop (ASUS TUF Gaming A15). The development roadmap includes multi-engine docking support (Smina, GNINA, QVina, LeDock) and molecular dynamics simulation capabilities, all permanently open-source and freely accessible without registration.