Interacting with the biomolecular solvent accessible surface via a haptic feedback device.

Area of Science:

• Biochemistry
• Computational Biology
• Molecular Visualization

Background:

• Computer-based molecular renderings have aided biomolecular research since the 1950s.
• Traditional 3D visualization relied on stereoscopic images and 3D displays.
• Haptic feedback devices offer potential for enhanced 3D molecular visualization.

Purpose of the Study:

• To develop a haptic rendering application for biomolecular visualization.
• To enhance three-dimensional awareness of biomolecular shape and surface accessibility.
• To explore the utility of haptic feedback in molecular graphics.

Main Methods:

• Developed a haptic rendering application (HaptiMol ISAS).
• Utilized a water molecule as a probe with hard-sphere interactions.
• Employed a 3D input device for molecular surface exploration.

Main Results:

• The application provides users with 3D awareness of biomolecular shape.
• Identified solvent-accessible regions and potential entropic bottlenecks.
• Discovered a narrow channel in liver alcohol dehydrogenase accessible only to single water molecules.
• Observed water molecules in sterically stable pockets on molecular surfaces.

Conclusions:

• HaptiMol ISAS enables exploration of biomolecular accessible surfaces using haptic feedback.
• Provides insights into molecular shape and water accessibility beyond conventional methods.
• Offers a novel approach to understanding biomolecular structure and function.