|
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
|
