AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking

Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications

(2016) Daniel Robinson et al.   Journal of Chemical Information and Modeling

Impact of Surface Water Layers on Protein–Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case?

(2016) Michael Betz 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

WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand–Receptor Docking

(2016) Robert B. Murphy et al.   JOURNAL OF MEDICINAL CHEMISTRY

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

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

Enthalpy–Entropy Compensation upon Molecular Conformational Changes

(2015) Mazen Ahmad et al.   Journal of Chemical Theory and Computation

Spatial Analysis and Quantification of the Thermodynamic Driving Forces in Protein–Ligand Binding: Binding Site Variability

(2015) E. Prabhu Raman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein–ligand docking using fitness learning-based artificial bee colony with proximity stimuli

(2015) Shota Uehara et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

PDB-wide collection of binding data: current status of the PDBbind database

(2014) Zhihai Liu et al.   BIOINFORMATICS

Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appendedlin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT)

(2014) Luzi J. Barandun et al.   CHEMISTRY-A EUROPEAN JOURNAL

AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins

(2014) Diogo Santos-Martins et al.   Journal of Chemical Information and Modeling

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

Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites

(2014) Daniel Alvarez-Garcia et al.   JOURNAL OF MEDICINAL CHEMISTRY

Incorporating replacement free energy of binding-site waters in molecular docking

(2014) Hanzi Sun et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin

(2013) Adam Biela et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules

(2013) Kamran Haider et al.   Journal of Chemical Information and Modeling

Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise

(2013) Ashutosh Kumar et al.   Journal of Chemical Information and Modeling

Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study

(2013) Andrea Bortolato et al.   Journal of Chemical Information and Modeling

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

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

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

Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

(2012) Xuan-Yu Meng et al.   Current Computer-Aided Drug Design

Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations

(2012) Miriam Sgobba et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Enthalpy–entropy compensation for some drugs dissociation in aqueous solutions

(2012) Milan Meloun et al.   FLUID PHASE EQUILIBRIA

Erratum: “Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril” [J. Chem. Phys. 137, 044101 (2012)]

(2012) Crystal N. Nguyen et al.   JOURNAL OF CHEMICAL PHYSICS

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Water Structure, Dynamics, and Spectral Signatures: Changes Upon Model Cavity–Ligand Recognition

(2012) Riccardo Baron et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking

(2011) Stefano Forli et al.   JOURNAL OF MEDICINAL CHEMISTRY

Analysis of water patterns in protein kinase binding sites

(2011) Caterina Barillari et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions

(2010) Sheng-You Huang et al.   Journal of Chemical Information and Modeling

Rapid Context-Dependent Ligand Desolvation in Molecular Docking

(2010) Michael M. Mysinger et al.   Journal of Chemical Information and Modeling

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

(2010) Dariusz Plewczynski et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Challenges and advances in computational docking: 2009 in review

(2010) Elizabeth Yuriev et al.   JOURNAL OF MOLECULAR RECOGNITION

Structural Properties of Hydration Shell Around Various Conformations of Simple Polypeptides

(2010) Dariusz Czapiewski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

The discovery and development of rivaroxaban, an oral, direct factor Xa inhibitor

(2010) Elisabeth Perzborn et al.   NATURE REVIEWS DRUG DISCOVERY

Nicotinic pharmacophore: The pyridine N of nicotine and carbonyl of acetylcholine hydrogen bond across a subunit interface to a backbone NH

(2010) A. P. Blum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: Analysis of the epidermal growth factor-like repeat A docking site using WaterMap

(2010) Robert A. Pearlstein et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Dewetting transitions in protein cavities

(2010) Tom Young et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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

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

Adding calorimetric data to decision making in lead discovery: a hot tip

(2009) John E. Ladbury et al.   NATURE REVIEWS DRUG DISCOVERY

Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography

(2009) M. Adachi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

(2009) Noriaki Okimoto et al.   PLoS Computational Biology

Investigation of MM-PBSA Rescoring of Docking Poses

(2008) David C. Thompson et al.   Journal of Chemical Information and Modeling

Assessment of programs for ligand binding affinity prediction

(2008) Ryangguk Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Exploiting Ordered Waters in Molecular Docking

(2008) Niu Huang 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