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

@article{citeulike:2185756, 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 macromolecules. 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.Program summary Title of program: ARVO Catalogue identifier: ADUL Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADUL Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Operating system under which the program has been tested: LINUX system and Windows system Programming language used: FORTRAN Computer: PC Pentium; SPP'2000; Number of bytes in distributed program, including test data, etc.: 322[thin space]633 Number of lines in distributed program, including test data, etc.: 5051 Distribution format: tar.gz Card punching code: ASCII Nature of physical problem: Molecular mechanics computations, continuum percolations. Method of solution: Numerical algorithm based on the analytical formulas, after using the stereographic transformation. Restriction on the complexity of the problem: The program does not account explicitly for cavities inside the molecule. Typical running time: Depends on the size of the molecule under consideration. Unusual features of the program: No}, author = {Busa, Jan and Dzurina, Jozef and Hayryan, Edik and Hayryan, Shura and Hu, Chin-Kun and Plavka, Jan and Pokorny, Imrich and Skrivanek, Jaroslav and Wu, Ming-Chya }, citeulike-article-id = {2185756}, doi = {http://dx.doi.org/10.1016/j.cpc.2004.08.002}, journal = {Computer Physics Communications}, keywords = {volume\_computation}, month = {January}, number = {1}, pages = {59--96}, posted-at = {2008-01-01 17:48:16}, priority = {2}, title = {ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations}, url = {http://dx.doi.org/10.1016/j.cpc.2004.08.002}, volume = {165}, year = {2005} }

TY - JOUR ID - citeulike:2185756 L3 - citeulike-article-id:2185756 TI - ARVO: A Fortran package for computing the solvent accessible surface area and the excluded volume of overlapping spheres via analytic equations JF - Computer Physics Communications VL - 165 IS - 1 SP - 59 EP - 96 N2 - 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 macromolecules. 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.Program summary Title of program: ARVO Catalogue identifier: ADUL Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADUL Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Operating system under which the program has been tested: LINUX system and Windows system Programming language used: FORTRAN Computer: PC Pentium; SPP'2000; Number of bytes in distributed program, including test data, etc.: 322[thin space]633 Number of lines in distributed program, including test data, etc.: 5051 Distribution format: tar.gz Card punching code: ASCII Nature of physical problem: Molecular mechanics computations, continuum percolations. Method of solution: Numerical algorithm based on the analytical formulas, after using the stereographic transformation. Restriction on the complexity of the problem: The program does not account explicitly for cavities inside the molecule. Typical running time: Depends on the size of the molecule under consideration. Unusual features of the program: No KW - volume_computation AU - Busa, Jan AU - Dzurina, Jozef AU - Hayryan, Edik AU - Hayryan, Shura AU - Hu, Chin-Kun AU - Plavka, Jan AU - Pokorny, Imrich AU - Skrivanek, Jaroslav AU - Wu, Ming-Chya PY - 2005/01/01/ UR - http://dx.doi.org/10.1016/j.cpc.2004.08.002 ER -