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Cup V OpenEye Scientific Software
CUP V Meeting
Feb 29-Mar 2, 2004
Santa Fe, NM
Cup V


Sunday, Feb. 29 (Sunset Room)
12.30-1.30 Check-In  
Gloves off.
Code, Chemistry and The American Way.
1.30 OEChem 1.2: Putting eyebrows on the Mona Lisa [HTML] [SXI] Matt Stahl
2.00 Shiny New Things, Glossy Old Things By:
QuackPack Geoff Skillman
CASE Matt Stahl
Szybki [HTML] [PPT] Stan Wlodek
OEFizzChem: ZAP, Grids, Surfaces.. [HTML] [PPT] Bob Tolbert
FRED 2.0 [HTML] [PPT] Mark McGann
Omega 1.8 Geoff Skillman
3.00 VIDA, Visualization and Visions [HTML] [PPT] Kevin Schmidt, Jon Christopher, Joe Corkery
3.30 Afternoon Tea
3.45 The Argument Sketch: Windows, SSSR, Planar Nitrogens, GBSA, Hydrogen Bonds, MDL Stereochemisry, Open Source, The Evil of Data Hierarchies, and the Perils of In-house Software Development... Cage Match
4.45 Break for Dinner
6.30 Mixer & Posters & Demos
  • Posters:
  • Demos:
    • InforSense KDE, demonstrating a workflow system incorporating data preparation and analysis tools for drug discovery, Brooke Magnanti, InforSense LLC.
    • Mesa AC, demo of tools described in poster above, Norah MacCuish et al.
    •, online OpenEye demos, Jeremy Yang, OpenEye.
8.30 Combinatorial mixology workshop (at bar).
Monday, Mar. 1 (Sunset Room)
Small molecules
Shape, Electrostatics, Shape and Electrostatics. Session chair: Anthony Nicholls
8.15 Tea, Coffee and Pastries.
9.00 ROCS 2.0: Adding Electrostatics to Shape [HTML] [PPT] Bob Tolbert
9.30 Universal Shape Fingerprints [HTML] [PPT] James Haigh, OpenEye/U. Sheffield
10.00 SAESAR: Shape and Electrostatics in SAR [HTML] [PPT] Norah and John MacCuish, Mesa Analytics
10.30 Mid-Morning Tea
10.45 Charges=Saruman, Radii=Sauron. Christopher Bayly, Merck-Frosst
11.15 Assessing and Extending Charging Models Andrew Grant, AstraZeneca
11.45 That darn pKa and tautomer problem. [HTML] [PPT] Geoff Skillman
12.15 Lunch: Seek and thou shalt find.
Lead Optimization, Molecular Properties, Chemical Feng Shui. Session chair: Peter Kenny
1.45 Drugs are good. (Good Drugs are better.) Pat Walters, Vertex Pharmaceuticals
2.15 Talking to Chemists: When louder isn't enough. [HTML] [PPT] Roger Sayle
2.45 Deep Shape Probes: How Big is Big Enough? Mike Tennant, Syrrx.
3.15 Why WABE is Brillig. [HTML] [PPT] Anthony Nicholls
3.45 MultiMolecule Superposition: The Application of Extreme Curvature Simon Kearsley, Merck
4.15 Time Out
5.00 The Levinthal Lecture: "Spacecraft, Washing Machines, Proteins.. Whatever." [HTML] [PPT 34MB!] Michael Sherman, Founder, Protein Mechanics
6.00 Clear on out
Tuesday, Mar. 2 (Sunset Room)
Big Molecules
Docking: What is it good for? Session chair: Steve Muchmore
8.15 Tea, Coffee and Pastries.
8.40 Docking: Huh! A Big Pharma Perspective Steve Muchmore, Abbott
9.00 Multiple Active Site Corrections for docking and virtual screening [HTML] [PPT] Guy Vigers, Array BioPharma
9.30 Promiscuity UnMASCed [HTML] [PPT] Ken Brameld, Celera Genomics
10.00 Pfiscore: Scoring by surface complementarity Lakshmi Narasimhan, Pfizer
10.30 Mid-Morning Tea
10.45 The Joy of High-Resolution Structures [HTML] [PPT] Yu Chen, UCSF
11.15 Protein Modes, Docking Woes Tomas Lundqvist, AstraZeneca
11.45 FRED and the future of docking [HTML] [PPT] Mark McGann
12.15 Lunch: You know the drill.
Proteins. Session chair: Janet Newman
1.45 The BDP: A Better Database of Proteins [HTML] [PPT] Tom Peat
2.05 "Sequence-Structure Alignment Tools from NCBI": Steve Bryant, NIH/NCBI/NLM
2.30 Proteins Abhorreth A Database: Roger Sayle
2.45 Afternoon Tea
3.00 Proteins, Membranes and Quantitative Electrostatics [HTML] [PPT] Diana Murray, Cornell University
3.30 Proteins are Charged: Get Over It! [HTML] [PPT] Marilyn Gunner, CUNY.
4.30 Grasping the Spicoli Toolkit [HTML] [PPT] Anthony Nicholls
5.00 Final Thoughts, Initial thoughts on CUP 6
5.10 Maximal dispersal to demos, mini-sessions and strategic think-tanks
6.30 You don't have to go home, but you can't stay here
7.00 Guadalajara Grill: Dinner on us
Wednesday, Mar. 3 (Sunset Room)
9-5 Training -- see separate schedule

Bonus presentation: MOL2 files for Dummies, Roger Sayle [HTML] [PPT]

What's new at CUP V?

OpenEye's mantra has always been that shape and electrostatics are crucial. CUP V will see many advances in elements of both:

  • We have expanded from shape only comparisons to the comparison of electrostatic fields with compelling results.
  • We have highly compressed electrostatic field storage suitable for databases.
  • We have accurate atomic charge assignment, and pKa and tautomer state enumeration.
  • We have advanced force-field implementations that provide reliable energies (with and without solvent) of molecules alone and in the active site of proteins.
  • We have begun to be expanded our approaches to proteins to include charging, pKa, structure optimization, and characterization of active site shape and electrostatics.
  • We have largely rewritten our visualization tools, and we have depiction and IUPAC offerings that will enhance most of our tools.

Also at CUP V, our academic and industrial users will give talks on an array of important topics, including

  • proper parameterization of Poisson-Boltzmann theory,
  • the application of Poisson-Boltzmann to docking,
  • the electrostatics of proteins,
  • the protein flexibility problem,
  • the application of shape as a molecular property through shape 'fingerprints',
  • extracting information from shape and electrostatic similarity,
  • the utility of docking and long-timescale molecular mechanics.

We expect you will find this program as interesting as we do and look forward to seeing you there!

-Anthony Nicholls

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