QligFEP: an automated workflow for small molecule free energy calculations in Q

Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms

(2018) Willem Jespers et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

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

Effect of Nitrogen Atom Substitution in A3 Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

(2017) Jhonny Azuaje et al.   JOURNAL OF MEDICINAL CHEMISTRY

Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton

(2017) Haiyang Zhang et al.   Journal of Physical Chemistry Letters

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

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

Structure-Based Rational Design of Adenosine Receptor Ligands

(2016) Hugo Gutiérrez-de-Terán et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

(2016) Lingle Wang et al.   Journal of Chemical Theory and Computation

GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

(2016) Mauricio Esguerra et al.   NUCLEIC ACIDS RESEARCH

The Chemical Space Project

(2015) Jean-Louis Reymond   ACCOUNTS OF CHEMICAL RESEARCH

Free energy calculations of A2A adenosine receptor mutation effects on agonist binding

(2015) Henrik Keränen et al.   CHEMICAL COMMUNICATIONS

FESetup: Automating Setup for Alchemical Free Energy Simulations

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

Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?

(2015) Shuai Liu et al.   Journal of Chemical Information and Modeling

Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field

(2015) Michael J. Robertson et al.   Journal of Chemical Theory and Computation

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

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

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

pmx: Automated protein structure and topology generation for alchemical perturbations

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

Structural and Energetic Effects of A2A Adenosine Receptor Mutations on Agonist and Antagonist Binding

(2014) Henrik Keränen et al.   PLoS One

Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors

(2014) Lars Boukharta et al.   PLoS Computational Biology

Characterization of the dynamic events of GPCRs by automated computational simulations

(2013) Hugo Gutiérrez-de-Terán et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Accuracy Assessment and Automation of Free Energy Calculations for Drug Design

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

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

(2013) Lingle Wang et al.   Journal of Chemical Theory and Computation

FEW: A workflow tool for free energy calculations of ligand binding

(2013) Nadine Homeyer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Lead optimization mapper: automating free energy calculations for lead optimization

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

Estimation of the size of drug-like chemical space based on GDB-17 data

(2013) P. G. Polishchuk et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

(2012) W. Liu et al.   SCIENCE

Brownian Dynamics Simulations of Ion Transport through the VDAC

(2011) Kyu Il Lee 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

Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

(2010) Julien Michel et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Good Practices in Free-Energy Calculations

(2010) Andrew Pohorille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cold Adaptation of Enzyme Reaction Rates†

(2008) Sinisa Bjelic et al.   BIOCHEMISTRY