Modelling of solvent positions around polar groups in proteins

Abstract

Previous analysis of the distribution of experimental solvent molecule positions around amino acid side chains showed that distinct clustering occurred close to polar or charged atoms in proteins. We have used those data to predict likely solvent positions around proteins not used in our initial analysis. We envisage that this algorithm, AQUARIUS, will be useful for finding solvent positions in electron density maps generated by protein crystallography and as useful starting positions for solvent molecules in computer simulation studies of macromolecules.