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Protein Sci. 2006 Nov;15(11):2525-33. Epub 2006 Sep 25.

A fast method for the determination of fractional contributions to solvation in proteins.

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  • 1Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biom├Ędica, Barcelona 08028, Spain.


A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Protein Data Bank allowed us to compute the expected fractional solvation of residues. This information is used to discuss when a residue or a group of residues presents an uncommon solvation profile.

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