Protein Structure Prediction: A Practical Approach
Protein Structure Prediction: A Practical Approach
Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins
IEEE Transactions on Parallel and Distributed Systems
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A new approach to identify solvent-exposed atoms in a protein and determine approximate locations of contacted water molecules is presented. The idea of the method is to generate for each atom of the protein molecule a surface grid consisting of twelve uniformly distributed points. These points describe potential locations of water molecules closely packed around an isolated atom. The grid surface coordinates are updated before each energy evaluation step by random rotation of the grid around the atom center. Each grid point is then checked with regard to its accessibility by water and the corresponding hydration status is assigned to it. Thus the information about the hydration degree of each protein atom and the positions of surrounding water molecules becomes available for energy evaluation procedure. Possible applications of the described method for implicit solvent models accounting for hydrophobic effect, electrical and van der Waals constituents of free energy of solvation, media-dependent electrical permittivity as well as hydrogen bonding with water are outlined.