SMART: a solvent-accessible triangulated surface generator for molecular graphics and boundary element applications

Area of Science:

• Computational chemistry
• Molecular modeling
• Computer-aided drug design

Background:

• Accurate representation of solvent-accessible molecular surfaces is crucial for understanding molecular interactions.
• Previous methods faced challenges in handling complex surface geometries, particularly in distorted regions like crevices and cavities.

Purpose of the Study:

• To present a novel algorithm, SMART (SMooth moleculAR surface Triangulator), for generating a smooth triangulated manifold representation of the solvent-accessible molecular surface.
• To improve the accuracy and robustness of molecular surface generation, especially in complex geometric areas.

Main Methods:

• The SMART algorithm divides the solvent-accessible molecular surface into curvilinear three-sided elements.
• It defines elements directly on appropriate geometric surface types, avoiding interpolation issues.
• Special features are incorporated to manage highly distorted regions within deep crevices and internal cavities.

Main Results:

• SMART generates a smooth, triangulated representation of the molecular surface.
• The algorithm effectively handles complex and distorted surface regions.
• It provides accurate computation of molecular surface areas and volumes.

Conclusions:

• The SMART algorithm offers an improved method for representing solvent-accessible molecular surfaces.
• This technique is valuable for boundary element methods in continuum electrostatics.
• It also aids in accurate surface area/volume calculations and generating shaded molecular displays for visualization.