Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations

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

D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

(2020) Conor D. Parks et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

An open-source drug discovery platform enables ultra-large virtual screens

(2020) Christoph Gorgulla et al.   NATURE

Rigorous Free Energy Simulations in Virtual Screening

(2020) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS)

(2020) Jan Walther Perthold et al.   Journal of Chemical Information and Modeling

Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials

(2020) Tai-Sung Lee et al.   Journal of Chemical Theory and Computation

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

(2020) Christina E. M. Schindler et al.   Journal of Chemical Information and Modeling

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

(2020) Tai-Sung Lee et al.   Journal of Chemical Information and Modeling

Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo

(2020) Gregory A. Ross et al.   Journal of Chemical Theory and Computation

Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease

(2020) Marina Macchiagodena et al.   Journal of Chemical Theory and Computation

Exploring Novel Directions in Free Energy Calculations

(2020) Kira A. Armacost et al.   Journal of Chemical Information and Modeling

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

Assessing the Predictive Power of Relative Binding Free Energy Calculations for Test Cases Involving Displacement of Binding Site Water Molecules

(2019) Joel Wahl et al.   Journal of Chemical Information and Modeling

Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo

(2019) Kalistyn H. Burley et al.   Journal of Chemical Theory and Computation

Simulating Water Exchange to Buried Binding Sites

(2019) Ido Y. Ben-Shalom et al.   Journal of Chemical Theory and Computation

Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations

(2019) Rajat K. Pal et al.   JOURNAL OF CHEMICAL PHYSICS

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

(2018) Samuel C. Gill et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

(2018) Wei Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry

(2017) Billy J. Williams-Noonan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

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

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation

(2017) Zhao X. Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding

(2017) M. Amaral et al.   Nature Communications

Sensitivity in Binding Free Energies Due to Protein Reorganization

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

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

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

Guidelines for the analysis of free energy calculations

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

pmx: Automated protein structure and topology generation for alchemical perturbations

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

Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

(2014) Marco D'Abramo et al.   Frontiers in Genetics

Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics

(2013) Christoph Dellago et al.   Entropy

Perspective: Alchemical free energy calculations for drug discovery

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

Protein Thermostability Calculations Using Alchemical Free Energy Simulations

(2010) Daniel Seeliger et al.   BIOPHYSICAL JOURNAL

Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies

(2010) Thomas Steinbrecher et al.   CURRENT MEDICINAL CHEMISTRY

λ-Dynamics free energy simulation methods

(2009) Jennifer L. Knight et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Statistically optimal analysis of samples from multiple equilibrium states

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