title: Robust classification of "relevant" water molecules in putative protein binding sites.
abstract: A statistically validated protocol to identify "relevant" water molecules in protein binding sites using HINT score and a geometric descriptor termed Rank is described. In training, conservation/nonconservation was modeled for 86% of the waters. For the test set, 87% of waters were correctly classified (92% when crystallographic resolution was <or=2.0 A). Conserved waters make at least two hydrogen bonds with protein and gain 0.6-2.0 kcal mol(-1) more binding energy than nonconserved waters.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Parma, Via G.P. Usberti 23/A, 43100 Parma, Italy.
authors.forename: Alessio
authors.initials: A
authors.lastname: Amadasi
authors.forename: J Andrew
authors.initials: JA
authors.lastname: Surface
authors.forename: Francesca
authors.initials: F
authors.lastname: Spyrakis
authors.forename: Pietro
authors.initials: P
authors.lastname: Cozzini
authors.forename: Andrea
authors.initials: A
authors.lastname: Mozzarelli
authors.forename: Glen E
authors.initials: GE
authors.lastname: Kellogg
mesh_terms: D001665:Binding Sites; D015195:Drug Design; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D008024:Ligands; D011506:Proteins; D014867:Water