Triangulation of molecular surfaces based on extracting surface atoms

•A novel real-time algorithm for surface atom extraction.•A method to subdivide the saddle patches into more uniform triangular meshes.•A new method to seamlessly join saddle patches to convex patches.

In this paper, we propose a novel surface atom extraction algorithm. By calculating the relative positions of the extended spheres, this algorithm detects all surface atoms reachable by the probe. Our algorithm overcomes the drawbacks of current methods and can be implemented in real time. This algorithm significantly improved the efficiency of calculating the solvent-excluded surface because only the values for the surface atoms are calculated instead of for all atoms. We also construct a triangular mesh model of the molecular solvent-excluded surface in terms of the surface atoms. By subdividing the saddle patches into more uniform triangular meshes, we improved the existing methods for triangulating a molecular surface composed of triangular concave spherical patches, saddle patches and convex patches. In addition, we introduce a new method that seamlessly joins saddle patches to convex patches.

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