AquaMMapS: An Alternative Tool to Monitor the Role of Water Molecules During Protein-Ligand Association

Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions

(2017) Juan Pablo Arcon et al.   Journal of Chemical Information and Modeling

Exploring Protein-Peptide Recognition Pathways Using a Supervised Molecular Dynamics Approach

(2017) Veronica Salmaso et al.   STRUCTURE

Deciphering the Complexity of Ligand–Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations

(2016) Alberto Cuzzolin et al.   Journal of Chemical Information and Modeling

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

(2016) Steven Ramsey et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Controlling the Dissociation of Ligands from the Adenosine A2A Receptor through Modulation of Salt Bridge Strength

(2016) Elena Segala et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure of the adenosine A2A receptor bound to an engineered G protein

(2016) Byron Carpenter et al.   NATURE

WATCLUST: a tool for improving the design of drugs based on protein-water interactions: Fig. 1.

(2015) Elias D. López et al.   BIOINFORMATICS

Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP

(2015) Alexander S. Bayden et al.   Journal of Chemical Information and Modeling

Perturbation of Fluid Dynamics Properties of Water Molecules during G Protein-Coupled Receptor–Ligand Recognition: The Human A2A Adenosine Receptor as a Key Study

(2014) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale

(2014) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

WATsite: Hydration site prediction program with PyMOL interface

(2014) Bingjie Hu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Profound Methyl Effects in Drug Discovery and a Call for New CH Methylation Reactions

(2013) Heike Schönherr et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Rapid parameterization of small molecules using the force field toolkit

(2013) Christopher G. Mayne et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Analysis of Biomolecular Solvation Sites by 3D-RISM Theory

(2013) Daniel J. Sindhikara et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water Networks Contribute to Enthalpy/Entropy Compensation in Protein–Ligand Binding

(2013) Benjamin Breiten et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Contributions of water transfer energy to protein-ligand association and dissociation barriers: Watermap analysis of a series of p38α MAP kinase inhibitors

(2013) Robert A. Pearlstein et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Solvent structure improves docking prediction in lectin–carbohydrate complexes

(2012) Diego F Gauto et al.   GLYCOBIOLOGY

Protein Pharmacophore Selection Using Hydration-Site Analysis

(2012) Bingjie Hu et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Methyl Effects on Protein–Ligand Binding

(2012) Cheryl S. Leung et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of 1,2,4-Triazine Derivatives as Adenosine A2A Antagonists using Structure Based Drug Design

(2012) Miles Congreve et al.   JOURNAL OF MEDICINAL CHEMISTRY

G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody

(2012) Tomoya Hino et al.   NATURE

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

(2012) Gregory A. Ross et al.   PLoS One

Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

(2012) W. Liu et al.   SCIENCE

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

MATCH: An atom-typing toolset for molecular mechanics force fields

(2011) Joseph D. Yesselman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Shielded Hydrogen Bonds as Structural Determinants of Binding Kinetics: Application in Drug Design

(2011) Peter Schmidtke et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation

(2011) Guillaume Lebon et al.   NATURE

Ligand binding to protein-binding pockets with wet and dry regions

(2011) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of an Agonist-Bound Human A2A Adenosine Receptor

(2011) F. Xu et al.   SCIENCE

Structure of the Adenosine A2A Receptor in Complex with ZM241385 and the Xanthines XAC and Caffeine

(2011) Andrew S. Doré et al.   STRUCTURE

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

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor

(2010) Christopher Higgs et al.   ACS Medicinal Chemistry Letters

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Prediction of the Water Content in Protein Binding Sites

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

Carbohydrate-Binding Proteins: Dissecting Ligand Structures through Solvent Environment Occupancy

(2009) Diego F. Gauto et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How druggable is protein kinase CK2?

(2009) Giorgio Cozza et al.   MEDICINAL RESEARCH REVIEWS

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures

(2008) Paul Labute   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist

(2008) V.-P. Jaakola et al.   SCIENCE