Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

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• 作者：Alessio Amadasi ; J. Andrew Surface ; Francesca Spyrakis ; Pietro Cozzini ; Andrea Mozzarelli ; Glen E. Kellogg
• 刊名：Journal of Medicinal Chemistry
• 出版年：2008
• 出版时间：February 28, 2008
• 年：2008
• 卷：51
• 期：4
• 页码：1063 - 1067
• 全文大小：465K
• 年卷期：v.51,no.4(February 28, 2008)
• ISSN：1520-4804

文摘

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 ≤2.0 Å). 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.