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Updated: Apr 4, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
AquaBridge: A novel method for systematic search of structural water molecules within the protein active sites
Arina Afanasyeva1,2, Sergey Izmailov3, Michel Grigoriev4,5
1Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University, Polytechnicheskaya, 29, Saint-Petersburg, 195251, Russia.
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.
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