Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

(2020) Andrea Rizzi et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software

(2020) Yuriy Khalak et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Comment on “Statistical efficiency of methods for computing free energy of hydration” [J. Chem. Phys. 149, 144111 (2018)]

(2019) Piero Procacci   JOURNAL OF CHEMICAL PHYSICS

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

(2019) Vytautas Gapsys et al.   eLife

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches

(2019) Matteo Aldeghi et al.   ACS Central Science

Estimation of Protein–Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations

(2019) Steffen Wolf et al.   Journal of Chemical Information and Modeling

Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations

(2018) Tomas Bastys et al.   Journal of Chemical Theory and Computation

SAMPL6 host–guest blind predictions using a non equilibrium alchemical approach

(2018) Piero Procacci et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Statistical efficiency of methods for computing free energy of hydration

(2018) Ahmet Yildirim et al.   JOURNAL OF CHEMICAL PHYSICS

Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas

(2018) Bernhard Knapp et al.   Journal of Chemical Theory and Computation

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation

(2018) Matteo Aldeghi et al.   ACS Central Science

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes

(2017) Vytautas Gapsys et al.   Journal of Chemical Theory and Computation

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

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

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan

(2016) Vytautas Gapsys et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Sensitivity in Binding Free Energies Due to Protein Reorganization

(2016) Nathan M. Lim et al.   Journal of Chemical Theory and Computation

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

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

(2016) Matteo Aldeghi et al.   Chemical Science

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Homologous ligands accommodated by discrete conformations of a buried cavity

(2015) Matthew Merski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pmx: Automated protein structure and topology generation for alchemical perturbations

(2014) Vytautas Gapsys et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

(2012) Vytautas Gapsys et al.   Journal of Chemical Theory and Computation

State-of-the-art in ligand-based virtual screening

(2011) Peter Ripphausen et al.   DRUG DISCOVERY TODAY

Protein Thermostability Calculations Using Alchemical Free Energy Simulations

(2010) Daniel Seeliger et al.   BIOPHYSICAL JOURNAL

Measuring the convergence of Monte Carlo free-energy calculations

(2010) Aljoscha M. Hahn et al.   PHYSICAL REVIEW E

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

(2009) Sarah E. Boyce et al.   JOURNAL OF MOLECULAR BIOLOGY

Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes

(2008) Maik Goette et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY