D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies

Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study

(2017) Henrik Keränen et al.   Journal of Chemical Theory and Computation

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors

(2017) Bernd Kuhn et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

(2017) Matteo Aldeghi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma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

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

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

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

(2016) Caitlin C. Bannan 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

Accurate calculation of the absolute free energy of binding for drug molecules

(2016) Matteo Aldeghi et al.   Chemical Science

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

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

The SAMPL4 host–guest blind prediction challenge: an overview

(2014) Hari S. Muddana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

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

Frontiers in free-energy calculations of biological systems

(2013) Christophe Chipot   Wiley Interdisciplinary Reviews-Computational Molecular Science

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: Combined Evaluation Across All Submitted Scoring Functions

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

Studies in mice, hamsters, and rats demonstrate that repression of hepatic apoA-I expression by taurocholic acid in mice is not mediated by the farnesoid-X-receptor

(2011) Christophe Gardès et al.   JOURNAL OF LIPID RESEARCH

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

(2010) Madhavi Sastry et al.   Journal of Chemical Information and Modeling

Analysis and comparison of 2D fingerprints: Insights into database screening performance using eight fingerprint methods

(2010) Jianxin Duan et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

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

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

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

(2009) Oleg Trott et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

(2008) Rommie E. Amaro et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN