Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

Blinded predictions of binding modes and energies of HSP90-α ligands for the 2015 D3R grand challenge

(2016) Antonia S.J.S. Mey et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Sensitivity in Binding Free Energies Due to Protein Reorganization

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

Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge

(2016) Stefano Bosisio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Overview of the SAMPL5 host–guest challenge: Are we doing better?

(2016) Jian Yin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blinded predictions of distribution coefficients in the SAMPL5 challenge

(2016) Stefano Bosisio et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

(2016) Yuan Hu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

(2016) Michael R. Shirts et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions

(2016) Symon Gathiaka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Elucidation of Nonadditive Effects in Protein–Ligand Binding Energies: Thrombin as a Case Study

(2016) Gaetano Calabrò et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

(2016) Stefania Evoli et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

FESetup: Automating Setup for Alchemical Free Energy Simulations

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

Evaluation of Selected Classical Force Fields for Alchemical Binding Free Energy Calculations of Protein-Carbohydrate Complexes

(2015) Sushil K. Mishra 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

Current and emerging opportunities for molecular simulations in structure-based drug design

(2014) Julien Michel   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

CASP10 results compared to those of previous CASP experiments

(2013) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Perspective: Alchemical free energy calculations for drug discovery

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

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

Optimization of a novel class of benzimidazole-based farnesoid X receptor (FXR) agonists to improve physicochemical and ADME properties

(2011) Hans G.F. Richter et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Alchemical free energy methods for drug discovery: progress and challenges

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

CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions

(2011) Richard D. Smith et al.   Journal of Chemical Information and Modeling

A Simple QM/MM Approach for Capturing Polarization Effects in Protein−Ligand Binding Free Energy Calculations

(2011) Frank R. Beierlein et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Discovery of novel and orally active FXR agonists for the potential treatment of dyslipidemia & diabetes

(2010) Hans G.F. Richter et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

(2010) James Luccarelli et al.   Journal of Chemical Theory and Computation

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

(2010) Wei Jiang et al.   Journal of Chemical Theory and Computation

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

Rigorous Free Energy Calculations in Structure-Based Drug Design

(2010) Julien Michel  et al.   Molecular Informatics

Identification of an N-oxide pyridine GW4064 analog as a potent FXR agonist

(2009) Song Feng et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Healthy skepticism: assessing realistic model performance

(2009) Scott P. Brown et al.   DRUG DISCOVERY TODAY

Prediction of the Water Content in Protein Binding Sites

(2009) Julien Michel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization

(2009) Julien Michel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Statistically optimal analysis of samples from multiple equilibrium states

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

Hit Identification and Binding Mode Predictions by Rigorous Free Energy Simulations

(2008) Julien Michel et al.   JOURNAL OF MEDICINAL CHEMISTRY

Optimization of Azoles as Anti-Human Immunodeficiency Virus Agents Guided by Free-Energy Calculations

(2008) Jacob G. Zeevaart et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Bornyl (3,4,5-trihydroxy)-cinnamate - An optimized human neutrophil elastase inhibitor designed by free energy calculations

(2007) Thomas Steinbrecher et al.   BIOORGANIC & MEDICINAL CHEMISTRY