ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations

Jan Buša, Jozef Džurina, Edik Hayryan, Shura Hayryan, Chin Kun Hu, Ján Plavka, Imrich Pokorńy, Jaroslav Skřivánek, Ming Chya Wu

Research output: Contribution to journalArticlepeer-review

33 Scopus citations

Abstract

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

Original languageEnglish
Pages (from-to)59-96
Number of pages38
JournalComputer Physics Communications
Volume165
Issue number1
DOIs
StatePublished - 1 Jan 2005

Fingerprint

Dive into the research topics of 'ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations'. Together they form a unique fingerprint.

Cite this