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ABSTRACT:
SUBMITTER: Schymkowitz JW
PROVIDER: S-EPMC1177371 | biostudies-literature | 2005 Jul
REPOSITORIES: biostudies-literature
Schymkowitz Joost W H JW Rousseau Frederic F Martins Ivo C IC Ferkinghoff-Borg Jesper J Stricher Francois F Serrano Luis L
Proceedings of the National Academy of Sciences of the United States of America 20050708 29
The empirical force field Fold-X was developed previously to allow rapid free energy calculations in proteins. Here, we present an enhanced version of the force field allowing prediction of the position of structural water molecules and metal ions, together called single atom ligands. Fold-X picks up 76% of water molecules found to interact with two or more polar atoms of proteins in high-resolution crystal structures and predicts their position to within 0.8 A on average. The prediction of meta ...[more]