Main (first) paper:
Ryan G. Coleman*, Michael Carchia, Teague Sterling, John J. Irwin, Brian K. Shoichet. Ligand Pose and Orientational Sampling in Molecular Docking. PLOS ONE. October 1, 2013. PDF. PubMed Central Free Full Text. Code. Documentation. Auto-DUD-E Test Set.
Paper on flexible docking: Marcus Fischer*, Ryan G. Coleman*, James S. Fraser, Brian K. Shoichet. Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nature Chemistry. Online May 25th, 2014.
Paper on using ChemAxon Marvin/cxcalc tool for protonation & reduced van der Waals grid size: Ryan G. Coleman*, Teague Sterling, Dahlia R. Weiss. SAMPL4 and DOCK3.7: lessons for automated docking procedures. Journal of Computer-Aided Molecular Design. March 1, 2014. Volume 28, Issue 3. PDF.