Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort

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

Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016

(2017) Xavier Fradera et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Assessing the Growth of Bioactive Compounds and Scaffolds over Time: Implications for Lead Discovery and Scaffold Hopping

(2016) Swarit Jasial et al.   Journal of Chemical Information and Modeling

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

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

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

Recent Advances in Scaffold Hopping

(2016) Ye Hu et al.   JOURNAL OF MEDICINAL CHEMISTRY

FESetup: Automating Setup for Alchemical Free Energy Simulations

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

Classification of Current Scoring Functions

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

Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment

(2015) Shunzhou Wan 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

Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models

(2015) Ming Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field

(2014) Timothy J. Giese et al.   ACCOUNTS OF CHEMICAL RESEARCH

Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set

(2014) Yan Li et al.   Journal of Chemical Information and Modeling

pmx: Automated protein structure and topology generation for alchemical perturbations

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

Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences

(2013) Art D. Bochevarov et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

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

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

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

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

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

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

(2010) Tyler Luchko et al.   Journal of Chemical Theory and Computation

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

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

Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor

(2009) K. Biggadike et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

(2008) Robert Abel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY