Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.

By Robert Abel, T. Young, R. Farid, B. Berne, Richard A. Friesner. Journal of the American Chemical Society, 2008

625 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Organic Chemistry

View Paper: https://www.semanticscholar.org/paper/d881c8736e2e41742797f952b0fb8ba3a6deb6e7

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In Computational Theory and Mathematics

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Citations in the corpus

Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap (2013, positive): “When the desolvation energy drives the ligand binding thermodynamics, the WaterMap analysis correlates well with binding free energies [11].”
AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking (2016, methodology): “Although the free energy change of displacing water can be calculated by GIST results directly, many previous studies reported that there was no direct correlation between the free energy of water molecules in the binding site and the affinity of bound ligands and that the use of the simplified scor”
Role of computer-aided drug design in modern drug discovery (2015, methodology): “Recently developed methods that take into account solvation contributions include WaterMap (Abel et al. 2008; Yang et al. 2013) and AcquaAlta (Rossato et al. 2011).”
Binding Affinity via Docking: Fact and Fiction (2018, methodology): “For instance, the Schrödinger’s WaterMap uses a short MD simulation and the estimation of the energies of the hydration sites are derived based on the simulation [48,50], whereas in the Molecular Operating Environment (MOE), the binding desolvation penalties can be estimated by 3D reference interact”
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get” (2009, neutral): “Perhaps ligands can be designed with improved affinities by recognizing nearby sites where waters can be easily displaced (Abel et al., 2008; Pan et al., 2007).”
Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review (2012, background): “Abel and coworkers have developed a unique approach WaterMap (49) to account for the contribution of the displacement of water molecules by ligand to binding free energy.”
Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances (2014, methodology): “Several methods have been developed to tackle this challenging problem, such as 3D RISM [17-19], SZMAP [20], JAWS [21], WaterMap [18, 22], which are utilized in commercial software [23-25].”