| Monday, March 6 |
| 8.00-9.00 Check in
|
| 8.15 |
Tea, Coffee and Pastries. |
|
| 8.45 |
Introduction to CUP
|
Anthony Nicholls, OpenEye
|
| 9.15 |
The OpenEye Development Plan
[PDF]
|
Bob Tolbert, OpenEye
|
| 10.30 |
Morning break |
|
| Session: The Government and
chemistry |
| 11.00 |
The NIH Molecular Libraries Initiative: Chemical Tools for the Genome Era
|
Chris Austin, NIH |
| 11.30 |
Carolina Exploratory Center for Cheminformatics Research: Development,
Implementation, and Use of the ChemBench system in support of NIH's
Molecular Library Initiative
|
Alex Tropsha, UNC |
| 12.00 |
Lunch |
| 1.00 |
Training: Shape searching with ROCS
[PDF]
tutorial[PDF]
|
Paul Hawkins, OpenEye |
| 2.30 |
Delineating the Underlying Chemistry and Physics of Small Molecules
Responsible for Biological Activity and Physical Properties
[abstract]
|
Anne Chaka, NIST |
| 3.00 |
Chemical Methodology and Library Development at Boston University
[abstract]
|
Scott Schaus, BU |
| 3.30 |
Chemical and Biological Analysis Tools in PubChem
[PDF]
|
Evan Bolton, NIH/NCBI |
| 4.00 |
Afternoon Tea |
|
| 4.15 |
InChI and other government conspiracies
[PDF]
|
Roger Sayle, OpenEye
|
| 4.45 |
Discussion: "On the role of government in drug discovery."
|
| Session -- Posters and Demos |
| 6.30-8.30 Open bar hosted by OpenEye
|
|
|
|
Posters: |
|
LexiChem and structure-based patent searching
[abstract]
|
Nicko Goncharoff, Reel Two
|
|
Chord fragment-based properties and fragment-key fingerprints
[abstract]
|
TJ O'Donnell, Gnova Scientific Software
|
|
Towards Shape Clustering of PubChem
[abstract]
|
Fabien Fontaine, Evan Bolton, Yulia Borodina and Stephen H Bryant, NIH/NCBI
|
|
Charting Biologically Relevant Chemical Space:
A Structural Classification of Natural Products (SCONP)
[abstract]
|
Wetzel, S., Ertl, P., Schuffenhauer, A., Waldmann, H.,
Max-Planck-Institute for Molecular Physiology
|
|
Generating Conformation Models using OMEGA:
Predicting RMSD needed for a desired number of conformers
[PNG]
|
Yulia Borodina, NIH/NCBI
|
|
Using search indexes to speed similarity neighboring
[PDF]
|
Evan Bolton, NIH/NCBI |
|
Implementing a text based method (Lingo) using Finite State
Machines for fast similarity searching
|
Andrew Grant, AstraZeneca;
James Haigh, Sheffield University;
Roger Sayle, OpenEye
|
|
Reproducing Bio-Active Conformations with Catalyst, Omega 2 and Macromodel
[abstract]
[PDF]
|
Johannes Kirchmair, University of Innsbruck;
Gerhard Wolber, Inte:Ligand GmbH;
Christian Laggner, University of Innsbruck;
Thierry Langer, University of Innsbruck
|
|
RMSD - Routine measure stirs doubts
[abstract]
[PNG]
addendum[PNG]
|
Jeremy Yang, OpenEye
|
|
One dimensional properties in virtual screening: can they be useful?
[PNG]
|
Paul Hawkins, OpenEye
|
|
|
|
| Demos: |
|
| 6.30 |
Surechem: LexiChem and structure-based patent searching |
Nicko Goncharoff, Reel Two |
| |
Chord
|
TJ O'Donnell, gNova |
| |
Stereo 3-D Visualization for Chemistry on Mac OS X
|
Matt MacInnis, Apple |
| |
The Cheminformatics Virtual Classroom
|
Norah and John MacCuish, Mesa |
| |
Vida |
Brian Kelley and Joe Corkery, OpenEye |
| |
SAESAR - Visualization of Shape Clusters
|
Mitch Chapman, Mesa |
| |
Afitt |
Jon Christopher, OpenEye |
| Tuesday, March 7 |
| 8.15 |
Tea, Coffee and Pastries. |
|
| Session: Bioisosteres |
| 8.45 |
Re-defining bio-isosterism using Rocs and Eon
[abstract]
[PDF]
|
Mike Tennant, Pharmix and Andy Jennings, Takeda |
| 9.15 |
Bioisoelektrofigosteres: Beyond what chemists already know?
[PDF 1.7 MB]
|
Geoff Skillman, OpenEye |
| 9.45 |
Application of EON for SAR Modeling and Bioisosteric Replacement
[PDF]
|
Zheng Yang, GSK |
| 10.15 |
Morning break |
|
| 10.45 |
Comprehensive enumeration of ligand shapes
|
James Haigh, Sheffield University |
| 11.15 |
Electrostatic similarity
[PDF] |
Anthony Nicholls, OpenEye |
| 11.45 |
Discussion: "Shape, Electrostatics, who could ask for
anything more?" |
| 12.00 |
Lunch |
| 1.00 |
Training: Docking with Fred
[PDF]
tutorial[PDF]
|
Paul Hawkins, OpenEye |
| Session: Ligand design |
| 2.30 |
Similarity of Molecular Surfaces: Tales of Multiple Scales
[PDF]
|
Ajay Jain, UCSF |
| 3.00 |
Integrating Virtual Screening Technologies (VST) with
High-Throughput Screening (HTS): Some Practical Examples
[abstract]
[PDF]
|
Tudor Oprea, UNM |
| 3.30 |
GLARE: Rough Cut-to-Shape for Truly Immense Libraries
|
Christopher Bayly, Merck Frosst |
| 4.00 |
Afternoon Tea |
|
| 4.30 |
ROCS and a small company: A success story in HCV
[abstract]
|
Dale Cameron, Migenix |
| 5.00 |
A comparison of structure-based and shape-based tools in virtual
screening
[PDF]
|
Paul Hawkins, OpenEye |
| 5.30 |
short break |
|
| 5.45 |
Levinthal Lecture: "Structure. Huh. What is it good for?"
|
Steve Muchmore, Abbott |
Wednesday, March 8th |
| 8.15 |
Tea, Coffee and Pastries. |
|
| Session: Simulations and Force
Fields |
| 8.45 |
Overview of Force Field Development
[abstract]
|
Wendy Cornell, Merck |
| 9.15 |
Putting statistical mechanics in its place: Using ensembles to
estimate binding affinities
|
Scott Brown, Abbott |
| 9.45 |
Lessons from massively-scaled free energy calculations on
Folding@Home
[abstract]
|
Michael Shirts, Columbia |
| 10.15 |
Morning break |
|
| 10.45 |
Your Tax Dollars at Work -- SimTK.org, really good free
software for physics-based simulation of biological structures
[abstract]
[PDF]
|
Michael Sherman, Stanford |
| 11.15 |
The OpenEye Plan for Binding Energies
|
Geoff Skillman, OpenEye |
| 11.45 |
Discussion: "Do we know enough to calculate Protein-Ligand
Affinities?"
|
| 12.00 |
Lunch |
| 1.00 |
Training: OEChem
[PDF]
examples
|
Jeremy Yang, OpenEye |
| Session: Structural biology |
| 2.30 |
Protein electrostatics
[PDF] |
Anthony Nicholls, OpenEye |
| 3.00 |
When gravity fails and negativity
does pull you through: Active site definition and manipulation
|
Marti Head, GSK and Kevin Schmidt, OpenEye |
| 3.30 |
An alternative approach for the evaluation of docking performance:
RMSD vs. RSR
[abstract]
[PDF]
|
Stefan Schmitt, AstraZeneca |
| 4.00 |
Afternoon Tea |
|
| 4.30 |
Real good real-space ligand density fitting |
Stan Wlodek and Brian Kelley, OpenEye |
| 5.00 |
More of the PDB's greatest mistakes
[PDF]
|
Matt Stahl, OpenEye |
| 5.30 |
Wrap up |
|
| 6:00 |
End of technical sessions |
| 7.00 | Dinner at the
Guadalajara Grill
(3788 Cerrillos Rd, 505-424-3544) -- hosted by OpenEye
|
|
|
|
![[PNG]](borodina/CUPVII_borodina.png){kind=link}
![[PNG]](jyang/JJ_RMSD.png){kind=link}
![addendum[PNG]](jyang/JJ_RMSD_addendum.png){kind=link}
![[PNG]](hawkins/Hawkins_UKqsar_06_ph.png){kind=link}