Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites

Docking-Based Comparative Intermolecular Contacts Analysis as New 3-D QSAR Concept for Validating Docking Studies and in Silico Screening: NMT and GP Inhibitors as Case Studies

(2011) Mutasem O. Taha et al.   Journal of Chemical Information and Modeling

AcquaAlta: A Directional Approach to the Solvation of Ligand–Protein Complexes

(2011) Gianluca Rossato et al.   Journal of Chemical Information and Modeling

A challenging system: Free energy prediction for factor Xa

(2011) Hannes G. Wallnoefer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Understanding Kinase Selectivity Through Energetic Analysis of Binding Site Waters

(2010) Daniel D. Robinson et al.   ChemMedChem

The Role of Water Molecules in Computational Drug Design

(2010) Stephanie de Beer et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Accounting for water molecules in drug design

(2010) Sergio E Wong et al.   Expert Opinion on Drug Discovery

Ligand−Protein Cross-Docking with Water Molecules

(2010) Ramasamy Thilagavathi et al.   Journal of Chemical Information and Modeling

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

(2010) James Luccarelli et al.   Journal of Chemical Theory and Computation

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

Biostructural and Pharmacological Studies of Bicyclic Analogues of the 3-Isoxazolol Glutamate Receptor Agonist Ibotenic Acid

(2010) Karla Frydenvang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Stabilizing of a Globular Protein by a Highly Complex Water Network: A Molecular Dynamics Simulation Study on Factor Xa

(2010) Hannes G. Wallnoefer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydration in Discrete Water. A Mean Field, Cellular Automata Based Approach to Calculating Hydration Free Energies

(2010) Piotr Setny et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex

(2010) Alfonso T. García-Sosa et al.   Molecular Informatics

Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6

(2009) Rita Santos et al.   Journal of Chemical Information and Modeling

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin

(2009) Abrar Hussain et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

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

Ligand Mapping on Protein Surfaces by the 3D-RISM Theory: Toward Computational Fragment-Based Drug Design

(2009) Takashi Imai et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ligand−Protein Docking with Water Molecules

(2008) Benjamin C. Roberts et al.   Journal of Chemical Information and Modeling

Exploiting Ordered Waters in Molecular Docking

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

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

(2008) Alessio Amadasi et al.   JOURNAL OF MEDICINAL CHEMISTRY

Involvement of Water in Carbohydrate−Protein Binding: Concanavalin A Revisited

(2008) Renuka Kadirvelraj et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY