Accounting for water molecules in drug design

The Role of Water Molecules in Computational Drug Design

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

Ligand−Protein Cross-Docking with Water Molecules

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

Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations

(2010) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs

(2009) Christopher R. Corbeil et al.   Journal of Chemical Information and Modeling

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

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

Prediction of the Water Content in Protein Binding Sites

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

The Properties of Water: Insights from Quantum Simulations†

(2009) Francesco Paesani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energies and Entropies of Water Molecules at the Inhibitor−Protein Interface of DNA Gyrase

(2009) Hongtao Yu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

High-energy water sites determine peptide binding affinity and specificity of PDZ domains

(2009) Thijs Beuming et al.   PROTEIN SCIENCE

Binding energy contributions of the conserved bridging water molecules in CDK2-inhibitor complexes: A combined QM/MM study

(2008) Ruo Jia et al.   CHEMICAL PHYSICS LETTERS

MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization

(2008) Cristiano R. W. Guimarães et al.   Journal of Chemical Information and Modeling

Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of Fitted1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors

(2008) Christopher R. Corbeil et al.   Journal of Chemical Information and Modeling

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

Impact of Plasticity and Flexibility on Docking Results for Cytochrome P450 2D6: A Combined Approach of Molecular Dynamics and Ligand Docking

(2008) Jozef Hritz 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

Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

(2008) Alan P. Graves et al.   JOURNAL OF MOLECULAR BIOLOGY

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

A structurally conserved water molecule in Rossmann dinucleotide-binding domains

(2002) Christopher A. Bottoms et al.   PROTEIN SCIENCE