Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

Uncertainty Quantification in Alchemical Free Energy Methods

(2018) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation

(2018) Laura Pérez-Benito et al.   Scientific Reports

Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study

(2017) Matteo Aldeghi et al.   Journal of Chemical Information and Modeling

Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation

(2017) Shunzhou Wan et al.   Journal of Chemical Information and Modeling

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study

(2017) Henrik Keränen et al.   Journal of Chemical Theory and Computation

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

(2017) Antonia S. J. S. Mey et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Overview of the SAMPL5 host–guest challenge: Are we doing better?

(2016) Jian Yin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

(2016) Bradley Sherborne et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy

(2016) Lili Duan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

1,500 scientists lift the lid on reproducibility

(2016) Monya Baker   NATURE

Accurate calculation of the absolute free energy of binding for drug molecules

(2016) Matteo Aldeghi et al.   Chemical Science

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

(2015) Shunzhou Wan 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

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors

(2014) David W. Wright et al.   Journal of Chemical Theory and Computation

Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations

(2013) Yong-Liang Zhu et al.   Journal of Chemical Information and Modeling

Explicit Ligand Hydration Shells Improve the Correlation between MM-PB/GBSA Binding Energies and Experimental Activities

(2013) Irene Maffucci et al.   Journal of Chemical Theory and Computation

Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity

(2012) Benjamin A. Hall et al.   BIOCHEMISTRY

The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant

(2012) Samuel Genheden et al.   Journal of Chemical Information and Modeling

Perspective: Alchemical free energy calculations for drug discovery

(2012) David L. Mobley et al.   JOURNAL OF CHEMICAL PHYSICS

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations

(2011) David W. Wright et al.   Journal of Chemical Information and Modeling

Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

(2011) Samuel Genheden et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs

(2011) S. Wan et al.   Journal of the Royal Society Interface

Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases

(2010) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations

(2010) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How to improve R&D productivity: the pharmaceutical industry's grand challenge

(2010) Steven M. Paul et al.   NATURE REVIEWS DRUG DISCOVERY

MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein−Protein Interface

(2009) Sergio Wong et al.   Journal of Chemical Theory and Computation

Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases

(2008) S. Kashif Sadiq et al.   Journal of Chemical Information and Modeling