View Talks from EuroCUP II
Program for CUP IX, held in Santa Fe, New Mexico, on March 17-19, 2008
Keynote Lecture:
A (Semi-Serious) Look at the State of Computational Life Science, Paul Labute, Chemical Computing Group
Sunday, March 16th, 2008
Toolkit Session
- 1:00 pm - 2:00 pm Sign In
Sunday Afternoon from 2pm - 5pm
- 2:00 Welcome, Bob Tolbert, OpenEye
- 2:10 MCSS in OEChem, Krisztina Boda, OpenEye [pdf 609 K]
- 2:30 Twisting OEShape, Kim Branson, Stanford University [pdf 1.5 MB]
3:00 Coffee Break
- 3:20 Applications of OEChem at Vertex, Pat Walters, Vertex Pharmaceuticals
- 3:50 Zap 2, Ben Ellingson, OpenEye [pdf 348 K]
- 4:10 Grids and Surfaces, Brian Cole, OpenEye [pdf 855 K]
- 4:30 Scripting in Vida, Joe Corkery, OpenEye [pdf 256 K]
5:00 End of Session
Monday, March 17th, 2008
8:00 am - 9:00 am: Sign-In
8:15 Tea & Pastries
Introduction
- 8:40 And Now, a Word from the President, Anthony Nicholls, OpenEye
Session 1: Shape & ES
- 9:00 Killing Two Birds with One Stone: Poisson's Equation for Accurate Polarizabilities and a Charge Model - Zap to the Global Parameterization, Jean-Francois Truchon, Université de Montréal and Merck Frosst
- 9:30 Utilization of OMEGA and ROCS to Calculate Molecule Queries and Alignments for Virtual Screening and Ligand-Based Design, Greg Tawa, Wyeth
10:00 - 10:30 Tea
- 10:30 Mathematics, Shape Space and Other Marriages Made in Heaven, Paul Hawkins, OpenEye [pdf 760 K]
- 11:00 Application of OE SHAPE ToolKit to Structure-Based Shape Pharmacophore Search, Jerry Ebalunode, NC Central University
- 11:30 PubChem3D: Relative Diversity of Shape (and Colour), Evan Bolton, NLM [pdf 480 K]
12:00 - 2:30 Lunch
Session 2: Structure—Can We Make It Useful for Drug Discovery?
- 2:30 A Quantum of Common Sense in Crystallography, Kennie Merz, QTP
- 3:00 Automated Structure Determination with Phenix, Ralf Grosse-Kunstleve, LBL
3:30 - 4:00 Tea
- 4:00 Field of Extremes: If You Re-refine It, They Will Come, Greg Warren, OpenEye, Manuel Perola, Vertex [pdf 1.2 MB]
- 4:30 Inching Towards a New Metric, Janet Newman, CSIRO
- 5:00 Protein Crystallographers: Sinners or Saints?, Gerard Kleywegt, Uppsala University
7:00 - 9:00 Open Bar and Poster Session
Posters
- Overcoming Challenges in the Communication of Chemical Information, Joe Corkery, Kevin Schmidt, Brian Kelley, OpenEye
- Virtual and Real Screenings: A Mixed Approach That Guided the Selection of Estrogen Receptors and Gpr30 Binders, Leitao Andrei, University of New Mexico
- OpenDLS: An Open Source Drug-Like Score, Oleg Ursu, University of New Mexico
- A Simple 2D Molecular Shape Similarity Method Enriches Biological Hits in Virtual Screening Experiments, Jerry Ebalunode, BRITE, North Carolina Central University
- Conformational Preferences Derived from Small Molecule Crystal Structures, Ken Brameld, Roche Palo Alto
- Application of the Concept of Shape Multipoles for 3D Molecular Similarity Search, Sunghwan Kim, National Center for Biotechnology Information
- A Optimally Efficient Method for Free Energy Calculations and Application to Ligand Binding Calculations, Michael Shirts, Columbia University
- Automation of Protein Structure Alignment and Visualization, Huifen Chen, Nicholas Skelton, Jeffery Blaney, Genentech Inc.
Tuesday, March 18th, 2008
8:00 am Tea & Pastries
Session 3: Lead Optimization Techniques. Evaluations
- 9:00 How Can We Integrate Computation into the Medicinal Chemistry Workflow?, Pat Walters, Vertex
- 9:30 Drug Guru: A Computational Tool that Uses Structural Transformations, Kent Stewart, Abbott Laboratories [pdf 1.4 MB]
10:00 - 10:30 Tea
- 10:30 Maximizing Lead Optimization Impact (Aligning Docking with Doctrine), Andy Good, BMS
- 11:00 FRED Is Not That Bad, Mark McGann, OpenEye
- 11:30 From Virtual Screening to Chemical Probes, Tudor Oprea, University of New Mexico
12:00 - 2:30 Lunch
Session 4: Stat techniques & Validation — New Window, Old Problems
- 2:30 Oh, What a Tangled Web We Weave When First We Practice to Believe: Chemical Similarity and Belief Theory-Based Data Fusion, Steve Muchmore, Abbott Laboratories
- 3:00 Docking Can Be Made To Suck Less Through a Series of Mind-Numbingly Arcane Innovations, John Irwin, UCSF
3:30 - 4:00 Tea
- 4:00 Lessons from Inductive Bias in Drug Design: Avoiding More Me-Too Drugs with 3D, Ajay Jain, UCSF
- 4:30 Drug Discovery - Lord, I Was Born a Gamblin' Man, Anthony Nicholls, OpenEye
5:30 The Levinthal Lecture: Paul Labute, Chemical Computing Group
A (Semi-Serious) Look at the State of Computational Life Science
Wednesday, March 19th, 2008
Session 5: SAMPL-1
- 8:45 Introduction: SAMPL1 - Failure is an Option, Anthony Nicholls, OpenEye
- 9:00 SAMPL1 at First Glance, Geoff Skillman, OpenEye [pdf 1 MB]
- 9:30 Samplin' Down South, Matt Geballe, Emory University
10:00 Tea
- 10:30 A SAMPLing of Different Methods for
Prospective Ligand Binding Calculation, Vijay Pande, John Chodera, Guha Jayachandran, Stanford
- 11:00 2D Control: Emulating the Algorithms Inside Chemists' Heads, Roger Sayle, OpenEye [pdf 440 K]
- 11:30 The Problem with Knowing Too Much, Marti Head, GSK
12:00 - 2:30 Lunch
- 2:30 Solvation Energies:
There are More out There Than We Thought, Peter Guthrie, U. of Western Ontario
- 3:00 And Miles to Go Before I Sleep, Enrico Purisima, BRI-NRCC
3:30 Tea
- 4:00 Predicting Hydration Free Energies and
Small Molecule Binding to Model Binding Sistes, Dave Mobley, UCSF
- 4:30 Da Mihi Castitatem et
Continentiam, Sed Moli Modo!, Anthony Nicholls, OpenEye
5:00 Panel Discussion
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