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QCMP164. 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.1It was developed
primarily tocalculatesurfacesfor
macromolecules, but it will work well with any
molecules 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
This program is derived from QCPE 566 which
originally worked on a computer with virtual
memory (VAX). In order to get USURF to fit into a
640-Kb-memory PC, certain changes in DIMENSION
statements had to be made. The following
parameters apply to this version of the program:
1. The maximum number of atoms has been
reduced to 4000.
2. The maximum number of probes is now 9000.
3. The maximum number of dots per sphere is
800.
References:
1. J. B. Moon and W. J. Howe, "A Fast Algorithm
for Generating Smooth Molecular Dot Surface
Representations," submitted to J. Mol.Graphics,
September, 1988.
2. M. J. Connolly, "Solvent-Accessible Surfaces
of Proteins and Nucleic Acids," Science, 221,
709-713.
3. B. Lee and F. M. Richards, "The
Interpretationof 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-l76.
Lines of Code: 780
Microsoft 5.1 (FORTRAN 77)
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