D3R Documents

D3R Overview Papers

Parks, C.D., Gaieb, Z., Chiu, M. et al. D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies. J Comput Aided Mol Des 34, 99–119 (2020). doi:10.1007/s10822-020-00289-y

Gaieb, Z., Parks, C.D., Chiu, M. et al. "D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings." J Comput Aided Mol Des (2019). doi:10.1007/s10822-018-0180-4

Gaieb, Z., Liu, S., Gathiaka, S. et al. "D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies." J Comput Aided Mol Des (2017). doi:10.1007/s10822-017-0088-4 additional Supplementary Information (PDF)

Gathiaka, S., Liu, S., Chiu, M. et al. "D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions." J Comput Aided Mol Des (2016) 30: 651. doi:10.1007/s10822-016-9946-8

Yin, J., Henriksen, N.M., Slochower, D.R. et al. "Overview of the SAMPL5 host-guest challenge: Are we doing better?" J Comput Aided Mol Des (2017) 31: 1. doi:10.1007/s10822-016-9974-4

Bannan, C.C., Burley, K.H., Chiu, M. et al. "Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge." J Comput Aided Mol Des 30 (2016): 927. doi:10.1007/s10822-016-9954-8

Special Journal Issues

Each special issue is a collection of papers written by challenge participants about their methods and results for a given challenge. This list of special issues currently is limited to challenges in which D3R played a role.

Grand Challenge 4, Part 1
Grand Challenge 4, Part 2
Grand Challenge 2
Grand Challenge 2015
SAMPL6
SAMPL5 host-guest challenge
SAMPL5 distribution coefficient challenge

CSAR Overview Papers

These articles derive from the prior CSAR project.

Carlson, Heather A. "Lessons Learned over Four Benchmark Exercises from the Community Structure-Activity Resource." Journal of Chemical Information and Modeling 56.6 (2016): 951-954. PMC. Web. 22 Feb. 2017. doi:10.1021/acs.jcim.6b00182

Carlson, H.A., Smith, R.D., Damm-Ganamet, K.L. "CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma." Journal of Chemical Information and Modeling 56.6 (2016): 1063-1077doi: 10.1021/acs.jcim.5b00523

Smith, Richard D., Kelly L. Damm-Ganamet, James B. Dunbar, Aqeel Ahmed, Krishnapriya Chinnaswamy, James E. Delproposto, Ginger M. Kubish, Christine E. Tinberg, Sagar D. Khare, Jiayi Dou, Lindsey Doyle, Jeanne A. Stuckey, David Baker, and Heather A. Carlson. "CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge." Journal of Chemical Information and Modeling 56.6 (2016): 1022-031. Web. doi: 10.1021/acs.jcim.5b00387

Damm-Ganamet, Kelly L., Richard D. Smith, James B. Dunbar, Jeanne A. Stuckey, and Heather A. Carlson. "CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series." Journal of Chemical Information and Modeling 53.8 (2013): 1853-870. Web. doi: 10.1021/ci400025f

Smith, Richard D., James B. Dunbar, Peter Man-Un Ung, Emilio X. Esposito, Chao-Yie Yang, Shaomeng Wang, and Heather A. Carlson. "CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions." Journal of Chemical Information and Modeling 51.9 (2011): 2115-131. Web. doi: 10.1021/ci200269q