AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA)

Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation

(2021) Germano Heinzelmann et al.   Scientific Reports

Variational Method for Networkwide Analysis of Relative Ligand Binding Free Energies with Loop Closure and Experimental Constraints

(2021) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis

(2021) Timothy J. Giese et al.   JOURNAL OF PHYSICAL CHEMISTRY A

CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER

(2021) Han Zhang et al.   Journal of Chemical Information and Modeling

FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations

(2021) Stamatia Zavitsanou et al.   Journal of Chemical Information and Modeling

PyAutoFEP: An Automated Free Energy Perturbation Workflow for GROMACS Integrating Enhanced Sampling Methods

(2021) Luan Carvalho Martins et al.   Journal of Chemical Theory and Computation

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

Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein–Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF

(2020) Xibing He et al.   ACS Omega

Validation of Free Energy Methods in AMBER

(2020) Hsu-Chun Tsai 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

Evolution of Alchemical Free Energy Methods in Drug Discovery

(2020) Lin Frank Song et al.   Journal of Chemical Information and Modeling

A fast and high-quality charge model for the next generation general AMBER force field

(2020) Xibing He et al.   JOURNAL OF CHEMICAL PHYSICS

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid

(2019) Victoria T. Lim et al.   Journal of Chemical Information and Modeling

Using AMBER18 for Relative Free Energy Calculations

(2019) Lin Frank Song et al.   Journal of Chemical Information and Modeling

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations

(2018) Haohao Fu et al.   Journal of Chemical Information and Modeling

A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method

(2018) Timothy J. Giese et al.   Journal of Chemical Theory and Computation

Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package

(2018) Daniel J. Mermelstein et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

(2018) Tai-Sung Lee et al.   Journal of Chemical Information and Modeling

Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges

(2018) Wei Chen et al.   Journal of Chemical Theory and Computation

Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database

(2017) Guilherme Duarte Ramos Matos et al.   JOURNAL OF CHEMICAL AND ENGINEERING DATA

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

(2017) Zoe Cournia et al.   Journal of Chemical Information and Modeling

Toward Fast and Accurate Binding Affinity Prediction with pmemdGTI: An Efficient Implementation of GPU-Accelerated Thermodynamic Integration

(2017) Tai-Sung Lee 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

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

(2017) Leela S. Dodda et al.   NUCLEIC ACIDS RESEARCH

FESetup: Automating Setup for Alchemical Free Energy Simulations

(2015) Hannes H. Loeffler et al.   Journal of Chemical Information and Modeling

Computational Calorimetry: High-Precision Calculation of Host–Guest Binding Thermodynamics

(2015) Niel M. Henriksen et al.   Journal of Chemical Theory and Computation

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins 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

A Python tool to set up relative free energy calculations in GROMACS

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

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

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

pmx: Automated protein structure and topology generation for alchemical perturbations

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

FreeSolv: a database of experimental and calculated hydration free energies, with input files

(2014) David L. Mobley et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations

(2014) Magnus Lundborg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Lead identification of novel and selective TYK2 inhibitors

(2013) Jun Liang et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Accuracy Assessment and Automation of Free Energy Calculations for Drug Design

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

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

Lead optimization mapper: automating free energy calculations for lead optimization

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

Lead Optimization of a 4-Aminopyridine Benzamide Scaffold To Identify Potent, Selective, and Orally Bioavailable TYK2 Inhibitors

(2013) Jun Liang et al.   JOURNAL OF MEDICINAL CHEMISTRY

Perspective: Alchemical free energy calculations for drug discovery

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

Alchemical free energy methods for drug discovery: progress and challenges

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

Efficient Drug Lead Discovery and Optimization

(2009) William L. Jorgensen   ACCOUNTS OF CHEMICAL RESEARCH

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B