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ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations. (English) Zbl 1196.92001

Summary: Ror calculating the solvation energy of proteins, hydration effects, drug binding, molecular docking, etc., it is important to have efficient and exact algorithms for computing the solvent accessible surface area and the excluded volume of macromolecules.We present a Fortran package based on new exact analytical methods for computing volume and surface areas of overlapping spheres. In this procedure the surface area and volume are expressed as surface integrals of the second kind over closed regions. Using stereographic projections the surface integrals are transformed to a sum of double integrals which are reduced to curve integrals. The MPI Fortran version is described as well. The package is also useful for computing the percolation probability of continuum percolation models.

MSC:

92-04 Software, source code, etc. for problems pertaining to biology
92C05 Biophysics
92C40 Biochemistry, molecular biology
60K35 Interacting random processes; statistical mechanics type models; percolation theory
92-08 Computational methods for problems pertaining to biology

Software:

SMMP; ARVO
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Full Text: DOI

References:

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