Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

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

Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen–Hydrogen Correlations

(2015) Camilo Velez-Vega et al.   Journal of Chemical Theory and Computation

Accurate Estimation of the Entropy of Rotation–Translation Probability Distributions

(2015) Federico Fogolari et al.   Journal of Chemical Theory and Computation

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Parameterization of an effective potential for protein-ligand binding from host-guest affinity data

(2015) Lauren Wickstrom et al.   JOURNAL OF MOLECULAR RECOGNITION

Interactions between Hofmeister Anions and the Binding Pocket of a Protein

(2015) Jerome M. Fox et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH

(2014) Camilo Velez-Vega et al.   Journal of Chemical Information and Modeling

Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm

(2014) David J. Huggins   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

WATsite: Hydration site prediction program with PyMOL interface

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

The Binding of Benzoarylsulfonamide Ligands to Human Carbonic Anhydrase is Insensitive to Formal Fluorination of the Ligand

(2013) Matthew R. Lockett et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

SPAM: A Simple Approach for Profiling Bound Water Molecules

(2013) Guanglei Cui et al.   Journal of Chemical Theory and Computation

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Comparing distance metrics for rotation using thek-nearest neighbors algorithm for entropy estimation

(2013) David J. Huggins   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure–Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis

(2012) Falgun Shah et al.   Journal of Chemical Information and Modeling

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

Free enthalpies of replacing water molecules in protein binding pockets

(2012) Sereina Riniker et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An overview of the Amber biomolecular simulation package

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

Contribution of Explicit Solvent Effects to the Binding Affinity of Small-Molecule Inhibitors in Blood Coagulation Factor Serine Proteases

(2011) Robert Abel et al.   ChemMedChem

Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase

(2011) P. W. Snyder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization

(2011) Thijs Beuming et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accounting for water molecules in drug design

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

A Displaced-Solvent Functional Analysis of Model Hydrophobic Enclosures

(2010) Robert Abel et al.   Journal of Chemical Theory and Computation

A Medicinal Chemist’s Guide to Molecular Interactions

(2010) Caterina Bissantz et al.   JOURNAL OF MEDICINAL CHEMISTRY

Water in Cavity−Ligand Recognition

(2010) Riccardo Baron et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Under water's influence

(2010) Gerhard Hummer   Nature Chemistry

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

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