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2009-04 | EuroCUP III | Toledo, ES

2009-04 | EuroCUP III | Toledo, ES

Toledo, Spain

April 22-23, 2009

Program for EuroCUP III, held in Toledo, Spain, April 22-24, 2009

Wednesday, April 22, 2009

Pre-meeting Toolkit Session

  • 9:30 What's New in OEChem, Bob Tolbert, OpenEye [pdf 694 K]
  • 10:00 MDL Query and Reaction Support in OEChem, Krisztina Boda, OpenEye
  • 10:30 Database Extensions for Fun and Profit, Andrew Dalke, Dalke Scientific Software AB

11:00 Morning Break

  • 11:30 Combining toolkits: Marriages made in Heaven, Paul Hawkins, OpenEye
  • 12:00 Scripting in Vida, Geoff Skillman, OpenEye

12:30 End of Toolkit Session & lunch

Session 1: Shape & Electrostatics

  • 15:30 ROCS and the ROCS Query Editor, Bob Tolbert, OpenEye [pdf 82 K]
  • 16:00 Karlsberg+ a Tool for Accurate pKa Computations in Proteins, Ernst-Walter Knapp, , Freie Universität Berlin
  • 16:30 Novel Approach for Chemotype Hopping Based on Annotated Database of Chemically Feasible Scaffolds and a Case Study, Julen Oyarzabal, CNIO

17:00 Afternoon Break

  • 17:30 Shape Descriptors: Sometimes Better than Nothing, Brian Kelley, OpenEye [pdf 1.95M]
  • 18:00 Shaping the Future of in silico Drug Design: Accurate Small-molecule Conformations from Experiment,Andrew Almond, Conformetrix Limited [pdf 5.88M]

18:30 End of session 1


  • Identification of Novel Scaffolds from an Original Chemical Library as Potential Antipsychotics, David Rodríguez, Fundación Pública Galega de Medicina Xenómica
  • Synthetic Accessibility and IP Protection in Fragment Based Design, Markus Gastreich, BioSolveIT
  • A comparison of ligand based virtual screening methods and application to corticotropin releasing factor 1 receptor,Gary Tresadern, Janssen Pharmaceutica
  • Mining Crystal Structure Databases for Compound Design, Andreas Steffen, Pfizer
  • Automated Navigation through the MedChem Space, Obdulia Rabal, Spanish National Cancer Research Centre
  • Conformer generation: Identifying and Learning from Failures, Paul Hawkins, OpenEye
  • Comparing Maximum Common Substructure Search Methods, Krisztina Boda, OpenEye
  • Canonical Isomeric Smiles Generation, Krisztina Boda, OpenEye
  • Rochambeau - Playing Games with ROCS, Imran Haque, Stanford University
  • GPUs: teraFLOPS, or teraFLAWED?, Imran Haque, Stanford University
  • High performance cheminformatics: Squeezing performance out of chemical file I/O, Bob Tolbert, OpenEye
  • gCOMBINE: A Graphical User Interface to Perform Structure-based Comparative Binding Energy (COMBINE) Analysis, Javier Klett, Centro de Biología Molecular Severo Ochoa

Thursday, April 23, 2009

Session 2: Fragment Design: Good Idea or the Latest Blind Alley?

  • 9:00 Challenges in Fragment-based Discovery, Roderick Hubbard, Vernalis [pdf 4.47M]
  • 9:30 Pharmacophore Development and NMR Validation of Small Fragments as Novel Heparanase Inhibitors,Rafael Gozalbes, CIPF [pdf 1.76M]
  • 10:00 Growing Fragments at UCB, Richard Taylor, UCB Celltech

10:30 Morning Break

  • 11:00 Multiple Roles of Computational Chemistry in Fragment Based Drug Design, Richard Law, Evotec
  • 11:30 Fragment-based Design: a Promising Strategy, Hugo Kubinyi, BASF [pdf 541K]
  • 12:00 FBDD, and Other Famous Land Wars in Asia, Peter Kenny, AstraZeneca, Anthony Nicholls, OpenEye

12:30 End of session 2 and lunch

14:00 OpenEye Product Demos, OpenEye

  • VIDA & VIVANT for Collaborative Visualization and Data Analysis
  • BROOD for Local Lead-Hopping With Shape and Electrostatics

Session 3: QSAR: Is it Worth it?

  • 15:00 Descriptor-based Modeling of Ligand Binding - An Illusion?, Dragos Horvath, University of Strasbourg [pdf 2.63M]
  • 15:30 AFMoCcon: Incorporating Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions, Holger Gohlke, Univ. of Düsseldorf [pdf 6.58M]
  • 16:00 A Reconsideration of the QSAR Methodology and of Parameterization in Molecular Modeling, Anthony Nicholls, OpenEye

16:30 End of session 3 and afternoon break

17:00 Castalian Allocution: What Should we Publish - or not? Thoughts on the Journal Landscape and Publication Culture in the CADD/Cheminformatics Field, Jürgen Bajorath, University of Bonn

Friday, April 24, 2009

Session 4: Databases and Data Sources for Molecular Modeling

  • 9:30 Iridium: Marginally Less Bad Than the Rest, Greg Warren, OpenEye [pdf 2.86M]
  • 10:00 Crystal Contacts and Ligand Binding: Implications for Scoring Functions, Jens Erik Nielsen, University College Dublin [pdf 10.6M]
  • 10:30 The Conversion of IUPAC's Compilations of pKas of Organic Acids and Bases into Substructure-searchable data, Tony Slater, pKaData Limited [pdf 255K]

11:00 Morning Break

  • 11:30 A Database of Dipoles: How Old-school Experiments Can Help New-school Methods, Andrew Grant, AstraZeneca
  • 12:00 View of an Outsider from the Inside: Ligand Treatment by the PDB, Terry Stouch, RCSB

12:30 End of session 4 — Concluding remarks, Anthony Nicholls, OpenEye

Lunch and departure