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566. USURF: Generation of Smooth Molecular Dot Surfaces
by J. B. Moon, The Upjohn Company, Kalamazoo, Michigan 49001 USURF is a FORTRAN program for generating smooth molecular dot surfaces.1 It was developed primarily to calculate surfaces for macromolecules, but it will work well with any molceules larger than around 30 atoms. USURF is intended to be a fast alternative to Connolly's MS program (QCPE 429)2 when only the graphical display of a molecular surface is needed. The algorithm is conceptually quite simple and proceeds in two steps. First, a "solvent-accessible"3 dot surface is calculated for a molecule. This is equivalent to a Van der Waals surface calculation in which each atomic radius has a solvent probe radius added to it. This surface can be regarded as a "solvation layer", in which each surface point represents the position of a solvent probe sphere in contact with the molecule. In the second step, the probe spheres are subjected to a Van der Waals dot surface calculation in which only the inward-facing hemispheres of each probe are surfaced. This second "van der Waals surface" is, in fact, a close approximation to a smooth "Richards surface"4. The simplicity of the calculations allows the program to run 2-6 times faster than MS. _____ References: 1. J. B. Moon and W. J. Howe, "A Fast Algorithm for Generating SmoothMolecularDotSurface Representations", submitted to J. Mol. Graphics, September, 1988. 2. M. L. Connolly, "Solvent-Accessible Surfaces of Proteins and Nucleic Acids", Science, 221, 709-713. 3. B. Lee and F. M. Richards, "The Interpretation of Protein Structures: Estimation of Static Accessibility", J. Mol. Biol., 55, 379-400. 4. F. M. Richards, "Areas, Volumes, Packing, and Protein Structure", Ann. Rev. Biophys. Bioeng., 6, 151-176. _____ FORTRAN 77 VAX Lines of Code: 780 |