Robust classification of "relevant" water molecules in putative protein binding sites.
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.
Amadasi
Alessio
A
Department of Biochemistry and Molecular Biology, University of Parma, Via G.P. Usberti 23/A, 43100 Parma, Italy.
Surface
J Andrew
JA
Spyrakis
Francesca
F
Cozzini
Pietro
P
Mozzarelli
Andrea
A
Kellogg
Glen E
GE
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*
D008024:Ligands; D011506:Proteins; D014867:Water