Affiliations

• Postdoctoral Fellow, Shoichet Lab
• Dept. of Pharmaceutical Chemistry
• University of California, San Francisco

Past Affiliations

• Kim Sharp Lab, Dept. of Biochemistry and Biophysics
• Ph.D., Genomics and Computational Biology
• School of Medicine, University of Pennsylvania

Upcoming Events

• ACS 245th National Meeting in New Orleans, Louisiana. I'll be speaking in the session on Protein-Ligand Interactions: Insights, New Tools and Applications in Drug Design, on the topic "Algorithms for discovering small molecules that stabilize specific protein conformations" at April 9, 2013 from 2:00 pm to 2:30 pm in Morial Convention Center, Room: 355. Link to the whole session

Recent Papers and Talks

• Ryan T. Cameron*, Ryan G. Coleman*, Jon P. Day, Krishna C. Yalla, Miles D. Houslay, David R. Adams, Brian K. Shoichet, George S. Baillie. Chemical informatics uncovers a new role for moexipril as a novel inhibitor of cAMP phosphodiesterase-4 (PDE4). Biochemical Pharmacology. 85(9), 1 May 2013, 1297-1305.

• John J. Irwin, Teague Sterling, Michael M. Mysinger, Erin S. Bolstad, Ryan G. Coleman. ZINC - A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling. 52(7). 1757-1768. July 23, 2012. PubMed Central Free Full Text.

• Jens Carlsson*, Ryan G. Coleman*, Vincent Setola*, John J. Irwin, Hao Fan, Avner Schlessinger, Andrej Sali, Bryan L. Roth, Brian K. Shoichet. Ligand Discovery from a Dopamine D3 Receptor Homology Model and Crystal Structure. Nature Chemical Biology. 7(11). 769-778. November 2011. PubMed Central Free Full Text. *Highlighted in Nature Reviews Drug Discovery. Charlotte Harrison. G protein-coupled receptors: Homology model allows effective virtual screening. 10, 816. 2011. *Curious Wavefunction Blog. *Faculty of 1000: Martin Stahl. 2011. http://f1000.com/13411085

• Ryan G. Coleman, Kim A. Sharp. Protein Pockets: Inventory, Shape, and Comparison. J. Chem. Inf. Model. 50(4). pp. 589-603. 26 April 2010. Supplemental Movie Alternate Movie Location PubMed Central Free Full Text. *Of Special Interest in: Current Opinion in Chemical Biology. Eric B. Fauman, Brajesh K. Rai, Enoch S. Huang. Structure-based druggability assessment--identifying suitable targets for small molecule therapeutics. 15(4). 2011.

• Ryan G. Coleman, Kim A. Sharp. Shape and evolution of thermostable protein structure. Proteins: Structure, Function, and Bioinformatics. 78(2). pp. 420-433. 1 February 2010. PubMed Central Free Full Text.

• Ryan G. Coleman, Kim A. Sharp. Finding and characterizing tunnels in macromolecules with application to ion channels and pores. Biophysical Journal. 96(2). pp 632-645. 21 January 2009. PubMed Central Free Full Text.

• Ryan G. Coleman, Kim A. Sharp. Travel Depth, a new shape descriptor for macromolecules: Application to ligand binding. Journal of Molecular Biology 362(3), pp. 441-458, 22 September 2006.

• Zelent, B., Vanderkooi, J.M., Coleman, R.G., Gryczynski, I., and Gryczynski Z. Protonation of excited state pyrene-1-carboxylate by phosphate and organic acids in aqueous solution studied by fluorescence spectroscopy. Biophysical Journal 91(10), pp. 3864-3871, November 2006. PubMed Central Free Full Text.

• Ryan G. Coleman, Michael A. Burr, Diane L. Souvaine, Alan C. Cheng. An intuitive approach to measuring protein surface curvature. Proteins: Structure, Function, and Bioinformatics. 61(4), Pages 1068-1074, 2005.

• Alan C. Cheng, Ryan G. Coleman, Kathleen T. Smyth, Qing Cao, Patricia Soulard, Daniel R. Caffrey, Anna C. Salzberg and Enoch S. Huang. Structure-based maximal affinity model predicts small-molecule druggability. Nature Biotechnology 25 (1), 71-75, 2007. *Highlighted in Nature Reviews Drug Discovery. Joanna Owens. Target Validation: Determining druggability 6, 187. 2007.

• Ryan G. Coleman, Anna C. Salzberg, Alan C. Cheng. Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model. J. Chem. Inf. Model. 46 (6), 2631-2637, 2006. *Predicted druggable binding site confirmed

• GCB/PCBI Retreat, May 24, 2012
• GPCR Workshop 2011
• Bob Parks and Ryan G. Coleman Helicopter Duration Model Descent Stability. National Association of Rocketry Annual Meet 53. Mason, Ohio. 2011. 1-32. 3rd place, Team Division. Video 1 Video 2
• Gordon Research Conference on Computer Aided Drug Design
• Bob Parks and Ryan G. Coleman The Pacific Flying Machines (PFM) Piston. National Association of Rocketry Annual Meet 52. Pueblo, Colorado. 2010. 1-24. 1st place, Team Division. Video 1 Video 2 Video 3 Video 4 Video 5 Video 6
• Dissertation Defense. Friday August 28th. 10:10 a.m. Class of '62 Auditorium, John Morgan Building. Shortest Geometric Paths Analysis in Structural Biology.
• Coleman, R.G. Why might heavier motors fly higher? National Association of Rocketry Annual Meet 51. Johnstown, Pennsylvania. 2009. 1-10. 1st place, C Division. Video
• Archived Talks & Meetings

Animations, Covers and other Art.

Code contributions: Travel Distance, DOCK 3.6, PFAAT

Co-Authors (38)

• David R. Adams, George S. Baillie, Erin S. Bolstad, Michael Branstein, Michael Burr, Daniel R. Caffrey, Ryan T. Cameron, Qing Cao, Jens Carlsson, Alan C. Cheng, W. Bruce Croft, Jon P. Day, Hao Fan, 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, 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.
• - Ryan Coleman
• ResearcherId - Ryan Coleman
• ClaimId - Ryan Coleman
• Twitter - @rgcjk
• UCSF Profiles - Ryan Coleman
• Epernicus - Ryan G. Coleman
• SelectedWorks - Ryan G. Coleman
• Google Scholar - Ryan G. Coleman (Google Scholar co-authors)
• PubMed/NCBI Publication List