Ranking docking poses by graph matching of protein–ligand interactions: lessons learned from the D3R Grand Challenge 2

The impact of in silico screening in the discovery of novel and safer drug candidates

(2017) Didier Rognan   PHARMACOLOGY & THERAPEUTICS

Lessons Learned over Four Benchmark Exercises from the Community Structure–Activity Resource

(2016) Heather A. Carlson   Journal of Chemical Information and Modeling

CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma

(2016) Heather A. Carlson et al.   Journal of Chemical Information and Modeling

Three-Dimensional Similarity in Molecular Docking: Prioritizing Ligand Poses on the Basis of Experimental Binding Modes

(2016) Andrew Anighoro et al.   Journal of Chemical Information and Modeling

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015

(2016) Inna Slynko 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

Structural Basis for Small Molecule NDB (N-Benzyl-N-(3-(tert-butyl)-4-hydroxyphenyl)-2,6-dichloro-4-(dimethylamino) Benzamide) as a Selective Antagonist of Farnesoid X Receptor α (FXRα) in Stabilizing the Homodimerization of the Receptor

(2015) Xing Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Knowledge-Based Strategy to Improve Ligand Pose Prediction Accuracy for Lead Optimization

(2015) Cen Gao et al.   Journal of Chemical Information and Modeling

CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge

(2015) Richard D. Smith et al.   Journal of Chemical Information and Modeling

POSIT: Flexible Shape-Guided Docking For Pose Prediction

(2015) Brian P. Kelley et al.   Journal of Chemical Information and Modeling

Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise

(2015) Ashutosh Kumar et al.   Journal of Chemical Information and Modeling

Beware of docking!

(2015) Yu-Chian Chen   TRENDS IN PHARMACOLOGICAL SCIENCES

Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes

(2014) Stefan Bietz et al.   Journal of Cheminformatics

CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series

(2013) Kelly L. Damm-Ganamet et al.   Journal of Chemical Information and Modeling

CSAR Data Set Release 2012: Ligands, Affinities, Complexes, and Docking Decoys

(2013) James B. Dunbar et al.   Journal of Chemical Information and Modeling

Encoding Protein–Ligand Interaction Patterns in Fingerprints and Graphs

(2013) Jérémy Desaphy et al.   Journal of Chemical Information and Modeling

A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function

(2012) Nadine Schneider et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes

(2011) James B. Dunbar et al.   Journal of Chemical Information and Modeling

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

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

Conformationally constrained farnesoid X receptor (FXR) agonists: Heteroaryl replacements of the naphthalene

(2010) Jonathan Y. Bass et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Assessment of programs for ligand binding affinity prediction

(2008) Ryangguk Kim et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY