2008-03 | CUP IX | Santa Fe, NM

Program for CUP IX

• Toolkit Session
  1:00-2:00 Sign In

  Sunday Afternoon from 2pm - 5pm

  • 2:00 Welcome, Bob Tolbert, OpenEye
  • 2:10 MCSS in OEChem, Krisztina Boda, OpenEye
  • 2:30 Twisting OEShape, Kim Branson, Stanford University 
  • 3:20 Applications of OEChem at Vertex, Pat Walters, Vertex Pharmaceuticals
  • 3:50 Zap 2, Ben Ellingson, OpenEye
  • 4:10 Grids and Surfaces, Brian Cole, OpenEye
  • 4:30 Scripting in VIDA, Joe Corkery, OpenEye

  5:00 End of Session

  Monday, March 17th, 2008

  8:00am - 9:00 Sign-in

  Introduction

  • 8:40 And Now, A Word from the President, Anthony Nicholls, OpenEye

  Shape 1: Shape & ES

  • 9:00 Killing Two Birds with One Stone:Poisson's Equation for Accurate Polarizations and a Charge Model - Zap to the Global Parameterization, Jean-Francois Truchon, Université de Montreal 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
  • 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

  12:00 - 12:30 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-Kunstieve, 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
  • 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

  • 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 Applications to Ligand Binding Calculations, Michael Shirts, Columbia University
  • Automation of Protein Structure Alignment and Visualization, Hulfen 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

  10:00 - 10:30 Lunch

  • 10:30 Maximizing Lead Optimization Impact (Aligning Docking with Doctrine), Andy Good, BMS
  • 11:00 FRED Is Not That Bad, Mark McGann, OpenEye

  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 Gambin' 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: SAMPL-1 - Failure is an Option, Anthony Nicholls, OpenEye
  • 9:00 SAMPL 1 at First Glance, Geoff Skillman OpenEye
  • 9:30 Samplin' Down South Matt Geballe, Emory University

  10:00 Tea

  • 10:30 A SAMPLing of Different Methods for Prospective Ligand Binding Calculations, Vijay Pande, John Chodera, Guha Jayachandran, Stanford
  • 11:00 2D Control: Emulating the Algorithms Inside Chemists' Heads, Roger Sayle, OpenEye
  • 11:30 The Problem with Knowing Too Much, Marti Head, GSK

  12:00 - 12:30 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