The role of water in ligand binding

Protein–Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals

(2020) Tobias Hüfner-Wulsdorf et al.   Journal of Chemical Information and Modeling

2-Substituted α,β-Methylene-ADP Derivatives: Potent Competitive Ecto-5′-nucleotidase (CD73) Inhibitors with Variable Binding Modes

(2020) Sanjay Bhattarai et al.   JOURNAL OF MEDICINAL CHEMISTRY

Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation

(2020) Yan Li et al.   Journal of Chemical Information and Modeling

Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome

(2020) Balázs Zoltán Zsidó et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structure of a DNA polymerase abortive complex with the 8OG:dA base pair at the primer terminus

(2020) Vinod K. Batra et al.   Communications Biology

Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules

(2019) Joel Wahl et al.   Journal of Chemical Information and Modeling

Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative

(2019) Katarina Koruza et al.   JOURNAL OF STRUCTURAL BIOLOGY

Network-based prediction of drug combinations

(2019) Feixiong Cheng et al.   Nature Communications

Diverse GPCRs exhibit conserved water networks for stabilization and activation

(2019) A. J. Venkatakrishnan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Water molecules in protein–ligand interfaces. Evaluation of software tools and SAR comparison

(2019) Eva Nittinger et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Characterization of hydration properties in structural ensemble of biomolecules

(2019) Mohan Pradhan et al.   Journal of Chemical Information and Modeling

Predicting Positions of Bridging Water Molecules in Nucleic Acid–Ligand Complexes

(2019) Wanlei Wei et al.   Journal of Chemical Information and Modeling

Broadly neutralizing anti-HIV-1 monoclonal antibodies in the clinic

(2019) Marina Caskey et al.   NATURE MEDICINE

Computational re-design of protein structures to improve solubility

(2019) Susanna Navarro et al.   Expert Opinion on Drug Discovery

Binding affinity in drug design: experimental and computational techniques

(2019) Visvaldas Kairys et al.   Expert Opinion on Drug Discovery

The current impact of water thermodynamics for small-molecule drug discovery

(2019) Stefan Geschwindner et al.   Expert Opinion on Drug Discovery

A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level

(2019) István Horváth et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Water in protein hydration and ligand recognition

(2019) Manuela Maurer et al.   JOURNAL OF MOLECULAR RECOGNITION

Water Networks Can Determine the Affinity of Ligand Binding to Proteins

(2019) John F. Darby et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Improving protein–ligand binding prediction by considering the bridging water molecules in Autodock

(2019) Qiangna Lu et al.   JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY

The role of water in amyloid aggregation kinetics

(2019) Amberley D Stephens et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Fast and Accurate Quantum Crystallography: From Small to Large, from Light to Heavy

(2019) Lorraine A. Malaspina et al.   Journal of Physical Chemistry Letters

Fast Microsecond Dynamics of the Protein–Water Network in the Active Site of Human Carbonic Anhydrase II Studied by Solid-State NMR Spectroscopy

(2019) Himanshu Singh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rethinking drug design in the artificial intelligence era

(2019) Petra Schneider et al.   NATURE REVIEWS DRUG DISCOVERY

X-rays in the Cryo-Electron Microscopy Era: Structural Biology’s Dynamic Future

(2018) Susannah C. Shoemaker et al.   BIOCHEMISTRY

Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations

(2018) Joel Wahl et al.   ChemMedChem

Advances in the treatment of explicit water molecules in docking and binding free energy calculations

(2018) Xiao Hu et al.   CURRENT MEDICINAL CHEMISTRY

Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods

(2018) Denis Bucher et al.   Journal of Chemical Information and Modeling

Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks

(2018) Axel Rudling et al.   Journal of Chemical Information and Modeling

Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox

(2018) Amanda Li et al.   JOURNAL OF CHEMICAL PHYSICS

Analysis of the influence of simulation parameters on biomolecule-linked water networks

(2018) Norbert Jeszenői et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings

(2018) Irene Maffucci et al.   Frontiers in Chemistry

Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples

(2018) Eva Nittinger et al.   Journal of Chemical Information and Modeling

Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site

(2018) Sonja Kunstmann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters

(2018) Jessica L. Thomaston et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Effective lead optimization targeting the displacement of bridging receptor–ligand water molecules

(2018) Deliang Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes

(2018) Johannes Schiebel et al.   Nature Communications

Analysis of solvent-exposed and buried co-crystallized ligands: a case study to support the design of novel protein–protein interaction inhibitors

(2018) Daniela Trisciuzzi et al.   DRUG DISCOVERY TODAY

Efficient and Accurate Hydration Site Profiling for Enclosed Binding Sites

(2018) Matthew R. Masters et al.   Journal of Chemical Information and Modeling

Testing inhomogeneous solvation theory in structure-based ligand discovery

(2017) Trent E. Balius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Water Determines the Structure and Dynamics of Proteins

(2016) Marie-Claire Bellissent-Funel et al.   CHEMICAL REVIEWS

Water, water, everywhere… It's time to stop and think

(2016) Michael S. Bodnarchuk   DRUG DISCOVERY TODAY

Exploration of Interfacial Hydration Networks of Target–Ligand Complexes

(2016) Norbert Jeszenői et al.   Journal of Chemical Information and Modeling

Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host–Guest Complexes

(2016) Haiyang Zhang et al.   Journal of Chemical Information and Modeling

Mobility-based prediction of hydration structures of protein surfaces

(2015) Norbert Jeszenői et al.   BIOINFORMATICS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

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

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

Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density

(2015) Eva Nittinger et al.   Journal of Chemical Information and Modeling

The solvent component of macromolecular crystals

(2015) Christian X. Weichenberger et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors

(2014) Stefan G. Krimmer et al.   ChemMedChem

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

(2014) Jean-François Truchon 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

Hydrogen-Bonded Water Molecules in the M2 Channel of the Influenza A Virus Guide the Binding Preferences of Ammonium-Based Inhibitors

(2014) Eleonora Gianti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition

(2012) Simon J. Elsässer et al.   NATURE

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

Water as an Active Constituent in Cell Biology

(2007) Philip Ball   CHEMICAL REVIEWS