Recent Papers

• Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. PDF. Code. Documentation. Cover Explanation. PubMed Central Free Full Text. *Highlighted by: Ligand discovery: Docking points.

• SAMPL4 and DOCK3.7: lessons for automated docking procedures. PDF. PubMed Central Free Full Text.

• Ligand Pose and Orientational Sampling in Molecular Docking. PDF. PubMed Central Free Full Text. Code. Documentation. Auto-DUD-E Test Set.

• Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4). PubMed Central Free Full Text.

• ZINC - A free tool to discover chemistry for biology. PubMed Central Free Full Text.

• Ligand Discovery from a Dopamine D3 Receptor Homology Model and Crystal Structure. PubMed Central Free Full Text. *Highlighted by: G protein-coupled receptors: Homology model allows effective virtual screening. *Highlighted by: http://f1000.com/13411085

• Protein Pockets: Inventory, Shape, and Comparison. Supplemental Movie Alternate Movie Location PubMed Central Free Full Text. *Of Special Interest by: Structure-based druggability assessment--identifying suitable targets for small molecule therapeutics.

• Shape and evolution of thermostable protein structure. PubMed Central Free Full Text.

• Finding and characterizing tunnels in macromolecules with application to ion channels and pores. PubMed Central Free Full Text.

• Structure-based maximal affinity model predicts small-molecule druggability. *Highlighted by Joanna Owens. Target Validation: Determining druggability

• Protonation of excited state pyrene-1-carboxylate by phosphate and organic acids in aqueous solution studied by fluorescence spectroscopy. PubMed Central Free Full Text.

• Travel Depth, a new shape descriptor for macromolecules: Application to ligand binding. Free Full Text

• Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model. *Predicted druggable binding site confirmed

• An intuitive approach to measuring protein surface curvature.

• Archived Talks & Meetings

Animations, Covers and other Art.

Code contributions: DOCK 3.7, Travel Distance, DOCK 3.6, PFAAT.
Github site.

Co-Authors (42)

• David R. Adams, George S. Baillie, Michael Branstein, Michael Burr, Daniel R. Caffrey, Ryan T. Cameron, Qing Cao, Michael Carchia, Jens Carlsson, Alan C. Cheng, W. Bruce Croft, Erin S. Davis, Jon P. Day, Hao Fan, Marcus Fischer, James S. Fraser, Ignacy Gryczynski, Zygmunt Gryczynski, Miles D. Houslay, Enoch S. Huang, John J. Irwin, Matthew King, Wei Li, Michael Mysinger, Bob Parks, David Pinto, Bryan L. Roth, Andrej Sali, Anna C. Salzberg, Avner Schlessinger, Vincent Setola, Kim A. Sharp, Brian K. Shoichet, Kathleen T. Smyth, Teague Sterling, Patricia Soulard, Diane L. Souvaine, Jane M. Vanderkooi, Xing Wei, Dahlia R. Weiss, Krishna C. Yalla, Bogumil Zelent.
• Google Scholar co-authors

Other Pages

• Tufts University - Ryan Coleman: I did my M.S. in Computer Science working with Diane L. Souvaine and Bruce M. Boghosian. My thesis was titled Finding knotted and linked vorticity lines in 3D vector fields.
• Google Scholar - Ryan G. Coleman (Google Scholar co-authors)
• Github - Ryan Coleman
• FigShare - Ryan Coleman