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Efficient Solvent Surface Computation in MSMS: Steps and Techniques

Explore Reduced Surface and Analytical SES computation with treatment of singularities, RS edges, vertices, and Free-RS edges. Learn about Triangulation of the Solvent-excluded surface and practical steps in MSMS algorithms. Discover the process for the Three Molecule Case RS computation, Binary Spatial Division Tree, and Triangulation strategies for the Five Molecule Case, including Toric and Spherical re-entrants. Complete your understanding of Solvent Surfaces with this comprehensive guide.

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Efficient Solvent Surface Computation in MSMS: Steps and Techniques

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  1. MSMS Algorithms John Korah

  2. SolventSurfaces

  3. Steps in MSMS • Reduced Surface computation • Analytical SES computation • Treatment of singularities • Triangulation of the Solvent excluded surface

  4. Reduced Surface

  5. Reduced Surface • RS- edges • RS- vertices • Fixed Position: The probe is simultaneously in touch with 3 or more atoms and cannot roll further without losing contact with at least one of the atoms. • Free-RS edge: if a probe can roll over a pair of atoms without colliding with a third atom, the RS edge joining the centers of these atoms is called the free-RS edge.

  6. Three Molecule Case

  7. RS computation • An initial F(c1,c2,c3) is selected (-one_cavity option) • Treatment of RS edge • Free RS edges • Free RS vertices-form components • Binary Spatial Division Tree-O(n log(n))

  8. Analytical SES computation • Spherical re-entrant face • Toric re-entrant face

  9. Five Molecule Case

  10. Triangulation of SES • Toric Reentrant is triangulated first. • Spherical reentrants and contact faces are triangulated by using template spheres

  11. Final Surface

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