A real-time proximity querying algorithm for haptic-based molecular docking

Area of Science:

• Computational chemistry and molecular modeling.
• Bioinformatics and drug discovery.
• Human-computer interaction and haptics.

Background:

• Intermolecular binding is fundamental to cellular processes and drug interactions.
• Molecular docking simulates these interactions in silico.
• Haptic-based docking enhances user interaction and intuition for accelerated docking.

Purpose of the Study:

• To develop an efficient real-time method for computing intermolecular forces in haptic-based molecular docking.
• To enable the modeling of molecular flexibility in interactive docking simulations.
• To create a user-friendly, accessible haptic docking solution.

Main Methods:

• Utilized octrees to decompose 3D search space for proximity querying of interacting atoms.
• Developed a dynamic tree construction and real-time force calculation method.
• Implemented the method in Haptimol_RD, a haptic-based, rigid-body molecular docking application.

Main Results:

• Achieved real-time computation of intermolecular forces for large molecular structures (thousands of atoms).
• Forces were computed within haptic refresh rates (1 kHz), enabling smooth manipulation.
• Demonstrated successful rigid-body docking using haptic feedback on consumer-level hardware.

Conclusions:

• The proposed octree-based proximity querying method efficiently computes intermolecular forces in real time.
• This approach overcomes limitations of pre-computed force grids, paving the way for flexible molecular docking.
• Haptimol_RD offers an accessible, immersive platform for molecular docking research.