Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands

The Role of Interfacial Water in Protein–Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force

(2018) Di Cui et al.   Journal of Chemical Theory and Computation

Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain

(2017) Germano Heinzelmann et al.   Journal of Chemical Theory and Computation

Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations

(2017) Bing Xie et al.   Journal of Chemical Theory and Computation

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

(2017) Federica Moraca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: Structural and thermodynamic modeling studies

(2016) Nanjie Deng et al.   PROTEIN SCIENCE

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

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

(2014) Emilio Gallicchio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Computational Study of Gleevec and G6G Reveals Molecular Determinants of Kinase Inhibitor Selectivity

(2014) Yen-Lin Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Free energetics of rigid body association of ubiquitin binding domains: A biochemical model for binding mediated by hydrophobic interaction

(2014) Di Cui et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase

(2014) Alison Slaughter et al.   Retrovirology

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Allosteric inhibition of HIV-1 integrase activity

(2013) Alan Engelman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

(2013) Gabriel J. Rocklin et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles

(2013) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation

(2013) Maria M. Reif et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Funnel metadynamics as accurate binding free-energy method

(2013) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Dual Role of Protein Phosphorylation in DNA Activator/Coactivator Binding

(2011) Voichita M. Dadarlat et al.   BIOPHYSICAL JOURNAL

Alchemical free energy methods for drug discovery: progress and challenges

(2011) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Elucidating the Energetics of Entropically Driven Protein–Ligand Association: Calculations of Absolute Binding Free Energy and Entropy

(2011) Nan-jie Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study

(2010) Nan-Jie Deng et al.   BIOPHYSICAL JOURNAL

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities

(2010) Emilio Gallicchio et al.   Journal of Chemical Theory and Computation

Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force

(2009) Slimane Doudou et al.   Journal of Chemical Theory and Computation

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

(2009) Yuqing Deng et al.   JOURNAL OF PHYSICAL CHEMISTRY B