Register for CUP X
Preliminary program for CUP X, 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
- 2:00 pm - 3:00 pm Sign In
- 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
- 5:00 Writing Multi-threaded OEChem with OpenMP, Brian Cole, OpenEye
- 5:30 Scripting in Vida 3.1, Joe Corkery, OpenEye
6:00 End of Session
Monday, March 9th, 2009 - Shape
8:00 am - 9:00 am: Sign-In
8:15 Tea & Pastries
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
- 10:50 Elucidating molecular overlays from pair-wise alignments using a genetic algorithm, Gareth Jones, Arena Pharmaceuticals
- 11:20 Shape, Pose Prediction and the American Way, Scott Brown, Abbott
12:00 - 2:30 Lunch
Lunchtime Product Training:
- 12:15 Science & Tools Overview: Lead Optimization, Greg Warren
- 1:15 VIDA & Vivant Demo, Joe Corkery, Kevin Schmidt & Phillip Sawunyama
Session 2:
- 2:30 Shape diversity in fragment library design, Ken Brameld, Roche
- 3:00 Masters of the Shape Universe, James Haigh, OpenEye/AstraZeneca
3:30 - 3:50 Tea
- 3:50 View of an outsider from the inside: Ligand treatment by the PDB, Terry Stouch, RCSB
- 4:20 Pre-computed 3D similarity of small molecules: PubChem 3D!, Evan Bolton, NCBI
- 4:50 Seeking a gold-standard for evaluating conformer ensembles, Paul Hawkins, OpenEye
6:30, Poster Session, Open Bar and Food
Posters
- 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
8:00 am Tea & Pastries
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 Modelling: 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
- 10.50 Shape(s) of Things, Ajay Jain, UCSF
- 11.25 The Levinthal Classic, Michael Sherman, Stanford
12:00 - 2:30 Lunch
Lunchtime Product Training:
- 12:15 Science & Tools Overview: Virtual Screening, Paul Hawkins
- 1:15 VIDA & Vivant Demo, Joe Corkery, Kevin Schmidt & Phillip Sawunyama
Session 4:
- 2.30 Docking - the Next 10 Years, Tack Kuntz, UCSF
- 3.05 Much Ado About Quantum Mechanics, Kennie Merz, QTP, University of Florida
3:40 - 4:00 Tea
- 4.00 Chemoinformatic and Structure-Based Screens for GPCR ligands, Brian Shoichet, UCSF
- 4.35 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:
- 8.50 Reprise
- 9.00 Considerations of small molecule strain energy, Johannes Hermann, Roche
- 9.30 Entropy in simulation & calorimetry, Demetri Moustakis, AstraZeneca
10:00 - 10:20 Tea
- 10.20 What did we learn about solvation energies from SAMPL-1?, Peter Guthrie, U. Western Ontario
- 10.50 Tautomers. Should you care? Yvonne Martin, Abbott
- 11.20 Montreal or Bust: SAMPL2, Geoff Skillman, OpenEye; Tom Peat, Janet Newman CSIRO, Melbourne
12:00 - 2:30 Lunch
Lunchtime Product Training:
- 12:15 Fun and Games with OpenEye Toolkits, Paul Hawkins & Brain Cole
Session 6:
- 2.30 If you can't even get the dipole right..., Andrew Grant, AstraZeneca
- 3.00 Electronic polarization from the internal continuum: an EPIC journey through the dielectric jungle, Jean-Francois Truchon, Merck Frosst
3:30 Tea
- 3.50 Restoring charge asymmetry in continuum electrostatics calculations of hydration free energies, Enrico Purisima, NRCC
- 4.20 Conformational dependent partial charges and why a dielectric might be your friend, Anthony Nicholls, OpenEye
- 4.50 What, oh what (if anything) are we going to do about force fields, Chris Bayly, Merck Frosst; Anthony Nicholls, OpenEye
6:30PM Conference Dinner: San Francisco St. Bar & Grill |
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