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2009-03 | CUP X | Santa Fe, NM

2009-03 | CUP X | Santa Fe, NM
Location:  Santa Fe, NM
Dates:  Mar 8-11, 2009

Program for CUP X, held in Santa Fe, New Mexico, on March 8-11, 2009

Keynote Lecture:

Is protein classification necessary? And other short stories spanning 40 years, Barry Honig, Columbia University 

Sunday, March 8th, 2009

Toolkit Session

  • 3:00 What's New in OEChem 1.7?, Bob Tolbert, OpenEye
  • 3:30 MDL Query and Reaction Support in OEChem, Krisztina Boda, OpenEye 
  • 4:00 Database extensions for fun and profit, Andrew Dalke, Andrew Dalke Scientific, AB

4:30 Tea

6:00 End of Session

Monday, March 9th, 2009 - Shape

Session 1:

  • 8:45 Introduction, Anthony Nicholls, OpenEye
  • 9:00 New Stuff. New people, new releases, new directions, Bob Tolbert, OpenEye
  • 9:15 ROCS and the ROCS Query Editor, Bob Tolbert, Kevin Schmidt, Anthony Nicholls, OpenEye
  • 9:45 Old Stuff. Ten years of CUP, Matt Stahl, OpenEye
  • 10:00 ROCS, je t'adore! Peut-être, Pat Walters, Vertex

10:30 - 10:50 Tea

Session 2:

3:30 - 3:50 Tea

6:30, Poster Session, Open Bar and Food


  • Iridium: A curated database of ligand-receptor complexes and binding data, Thahn Do, Stephen Warren, Gonzaga
  • Rochambeau: Playing Games with ROCS, Imran Haque, Stanford
  • Web application development for research cheminformatics, Jeremy Yang, UNM
  • Statistical analysis of virtual screening, Mark McGann, OpenEye
  • Perception and representation of alternate conformers in OEChem, Mike Word, OpenEye
  • Shape multipoles and other approximate shape methods, Brian Kelley, OpenEye
  • Exploiting GPCR Activity Data En Masse: GA-Focused Descriptor Active Subspace (GAFDAS), Carleton Sage, Arena Pharmaceuticals
  • Comparing Maximum Common Substructure Search Methods, Krisztina Boda, OpenEye
  • Canonical Isomeric Smiles Generation, Krisztina Boda, OpenEye
  • High performance cheminformatics: Squeezing performanc out of chemical file I/O, Brian Cole, OpenEye
  • Visualizing charge density and solvation energy on a grid, Ben Ellingson, OpenEye
  • ROCS Color is boring. Is that a good thing? Discuss, Kim Branson, Stanford
  • Non-bulk-like solvent in the ribosome exit tunnel, Del Lucent, Stanford
  • Entropic contributions to binding and transfer., Stan Wlodak, OpenEye
  • Bench: Developing a cheminformatics platform using Eclipse RCP and OpenEye software, Paul Watson, Arena Pharmaceuticals
  • Shape and Color Clustering with SAESAR, Norah MacCuish, Mesa Analytics
  • Novel Applications of Python in Computational Chemistry Workflows, Alexander Bayden, Virginia Commonwealth University
  • Evaluation of DOCK for Reproducing Crystallographic Binding Poses, Sudipto Mukherjee, Trent E. Balius, and Robert C. Rizzo, Stony Brook University
  • Choosing Floating Point Models for Reproducibility or Performance, Ronald Green, Intel Corporation

Tuesday, March 10th, 2009 - The Levinthal Day

Session 3:

  • 8:40 Reprise
  • 8.45 All the truth in the world adds up to one big lie: the need for significantly improved analysis of experimental and computational data., Vijay Pande, Stanford
  • 9.20 Lies, Damned Lies, and Molecular Modeling: It's Almost Always Worse Than You Think, Steve Muchmore, Abbott
  • 9.55 Why is Quantum Mechanics not more useful?, Tom Darden, OpenEye 

10:30 - 10:50 Tea

Session 4:

3:40 - 4:00 Tea

  • 4.00 Protonate3D Assignment of Protonation State and Geometry in Macromolecular Structures, Paul LaBute, CCG

5:30 The Levinthal Lecture: Barry Honig, Columbia University
Is protein classification necessary? And other short stories spanning 40 years

Wednesday, March 11th, 2009 - Electrostatics

Session 5:

10:00 - 10:20 Tea

Session 6:

3:30 Tea