Assessing the stability of free-energy perturbation calculations by performing variations in the method

Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies

(2017) Martin A. Olsson et al.   Journal of Chemical Theory and Computation

D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2017) Zied Gaieb et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Galectin-3-Binding Glycomimetics that Strongly Reduce Bleomycin-Induced Lung Fibrosis and Modulate Intracellular Glycan Recognition

(2016) Tamara Delaine et al.   CHEMBIOCHEM

Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration

(2016) Agastya P. Bhati et al.   Journal of Chemical Theory and Computation

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level

(2016) Martin A. Olsson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

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

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

(2015) Edward Harder et al.   Journal of Chemical Theory and Computation

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

(2015) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

A Large-Scale Test of Free-Energy Simulation Estimates of Protein–Ligand Binding Affinities

(2014) Paulius Mikulskis et al.   Journal of Chemical Information and Modeling

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

(2014) Paulius Mikulskis et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Regulation of Alternative Macrophage Activation by Galectin-3

(2014) A. C. MacKinnon et al.   JOURNAL OF IMMUNOLOGY

Accuracy Assessment and Automation of Free Energy Calculations for Drug Design

(2013) Clara D. Christ et al.   Journal of Chemical Information and Modeling

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

(2013) Samuel Genheden et al.   Journal of Chemical Theory and Computation

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package

(2013) Joseph W. Kaus et al.   Journal of Chemical Theory and Computation

Lead optimization mapper: automating free energy calculations for lead optimization

(2013) Shuai Liu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Improving the Efficiency of Protein–Ligand Binding Free-Energy Calculations by System Truncation

(2012) Samuel Genheden et al.   Journal of Chemical Theory and Computation

Can the protonation state of histidine residues be determined from molecular dynamics simulations?

(2012) Jon Uranga et al.   Computational and Theoretical Chemistry

Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA

(2011) Samuel Genheden et al.   Journal of Chemical Information and Modeling

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

(2011) Thomas Steinbrecher et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

(2011) Jeff Wereszczynski et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Galectins: regulators of acute and chronic inflammation

(2010) Fu-Tong Liu et al.   Annals of the New York Academy of Sciences

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

Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations

(2010) Samuel Genheden et al.   Journal of Chemical Theory and Computation

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

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

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir

(2009) Morgan Lawrenz et al.   Journal of Chemical Theory and Computation

How to obtain statistically converged MM/GBSA results

(2009) Samuel Genheden et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Role of Galectins in Protein Trafficking

(2009) Delphine Delacour et al.   TRAFFIC

Theoretical and Practical Considerations in Virtual Screening: A Beaten Field?

(2008) Maria Kontoyianni et al.   CURRENT MEDICINAL CHEMISTRY

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS