AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites

Journal of Computational Chemistry
Arina AfanasyevaMichael Petukhov

Abstract

We have developed a novel method for calculation of the water bridges that can be formed in the active sites of proteins in the absence or in the presence of small-molecule ligands. We tested its efficiency on a representative set of human ATP-binding proteins, and show that the docking accuracy of ligands can be substantially improved when water bridges are included in the modeling of protein-ligand interactions. Our analysis of binding pocket hydration can be a useful addition to the in silico approaches of Drug Design.

References

Jan 1, 1997·Annual Review of Pharmacology and Toxicology·T J MarroneJ A McCammon
Nov 5, 1999·Protein Science : a Publication of the Protein Society·M PetukhovL Serrano
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Jan 4, 2003·Journal of Computer-aided Molecular Design·Ricardo L Mancera
Jul 9, 2004·Protein Science : a Publication of the Protein Society·Michael PetukhovLuis Serrano
Dec 13, 2006·Journal of Medicinal Chemistry·Niu HuangJohn J Irwin
Feb 13, 2008·Journal of the American Chemical Society·Robert AbelRichard A Friesner
Sep 26, 2009·Journal of the American Chemical Society·Julien MichelWilliam L Jorgensen
Mar 19, 2014·Journal of Chemical Theory and Computation·Jean-François TruchonPaul Labute
Dec 10, 2013·Journal of Chemical Theory and Computation·Guanglei CuiEric S Manas

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