Evaluation of water displacement energetics in protein binding sites with grid cell theory

Strategies to Calculate Water Binding Free Energies in Protein–Ligand Complexes

(2014) Michael S. Bodnarchuk et al.   Journal of Chemical Information and Modeling

A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies

(2014) Jean-François Truchon et al.   Journal of Chemical Theory and Computation

Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design

(2014) Daniel Alvarez-Garcia et al.   Journal of Chemical Theory and Computation

Macromolecular Entropy Can Be Accurately Computed from Force

(2014) Ulf Hensen et al.   Journal of Chemical Theory and Computation

Evaluation of Host–Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory

(2014) Julien Michel et al.   Journal of Chemical Theory and Computation

Variational Implicit Solvation with Poisson–Boltzmann Theory

(2014) Shenggao Zhou et al.   Journal of Chemical Theory and Computation

Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa

(2014) Crystal N. Nguyen et al.   Journal of Chemical Theory and Computation

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling

(2014) Wenbo Yu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites

(2014) Daniel Alvarez-Garcia et al.   JOURNAL OF MEDICINAL CHEMISTRY

Current and emerging opportunities for molecular simulations in structure-based drug design

(2014) Julien Michel   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

(2013) Katrina W. Lexa et al.   Journal of Chemical Information and Modeling

Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory

(2013) Georgios Gerogiokas et al.   Journal of Chemical Theory and Computation

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

(2012) Crystal N. Nguyen et al.   JOURNAL OF CHEMICAL PHYSICS

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Spirocyclic Sulfamides as β-Secretase 1 (BACE-1) Inhibitors for the Treatment of Alzheimer’s Disease: Utilization of Structure Based Drug Design, WaterMap, and CNS Penetration Studies To Identify Centrally Efficacious Inhibitors

(2012) Michael A. Brodney et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

(2010) Daniel Seeliger et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

(2010) Julien Michel et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Discovery of (2,4-Dihydroxy-5-isopropylphenyl)-[5-(4-methylpiperazin-1-ylmethyl)-1,3-dihydroisoindol-2-yl]methanone (AT13387), a Novel Inhibitor of the Molecular Chaperone Hsp90 by Fragment Based Drug Design

(2010) Andrew J. Woodhead et al.   JOURNAL OF MEDICINAL CHEMISTRY

Rigorous Free Energy Calculations in Structure-Based Drug Design

(2010) Julien Michel  et al.   Molecular Informatics

Prediction and interpretation of the hydration entropies of monovalent cations and anions

(2010) Sheeba Jem Irudayam et al.   MOLECULAR PHYSICS

Entropic trends in aqueous solutions of the common functional groups

(2009) Sheeba Jem Irudayam et al.   FARADAY DISCUSSIONS

Prediction of the Water Content in Protein Binding Sites

(2009) Julien Michel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Entropic Cost of Protein−Ligand Binding and Its Dependence on the Entropy in Solution

(2009) Sheeba Jem Irudayam et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

(2009) Julien Michel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exploiting Ordered Waters in Molecular Docking

(2008) Niu Huang et al.   JOURNAL OF MEDICINAL CHEMISTRY