Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors

(2017) Marc van Dijk et al.   Journal of Chemical Information and Modeling

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

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

Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation

(2015) Luigi Capoferri et al.   PLoS One

Identification of trisubstituted-pyrazol carboxamide analogs as novel and potent antagonists of farnesoid X receptor

(2014) Donna D. Yu et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

(2014) C. Ruben Vosmeer et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Applicability Domain Analysis (ADAN): A Robust Method for Assessing the Reliability of Drug Property Predictions

(2014) Pau Carrió et al.   Journal of Chemical Information and Modeling

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context

(2014) Nadine Homeyer et al.   Journal of Chemical Theory and Computation

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

(2013) Lovorka Perić-Hassler et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

Comparison of Different Approaches to Define the Applicability Domain of QSAR Models

(2012) Faizan Sahigara et al.   MOLECULES

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

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

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

Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes

(2010) Eva Stjernschantz et al.   BIOPHYSICAL JOURNAL

ParaDockS: A Framework for Molecular Docking with Population-Based Metaheuristics

(2010) René Meier et al.   Journal of Chemical Information and Modeling

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

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

Identification of a potent synthetic FXR agonist with an unexpected mode of binding and activation

(2008) S. M. Soisson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA