Schedule for InnovationWell and eCheminfo Autumn 2008 Community of Practice Meeting

I provide below a schedule for the upcoming InnovationWell and eCheminfo Community of Practice meetings at Bryn Mawr.

I also include a location map here which may be useful upon arrival:

Download bryn_mawr_campus_map_douglas_connect_meeting.pdf

[Please follow continuation here to view schedule.]

Chemogenomics eCheminfo cheminformatics chemoinformatics bioinformatics Medicinal Chemistry Computational Chemistry Virtual Screening Molecular Modelling Molecular Modeling pharmaceutical pharma meeting workshop training Oxford Critical Path toxicology Bursary Life Sciences Pharma Drug Discovery Research and Development Drug Development Healthcare Innovation Knowledge Management events

InnovationWell - eCheminfo Community Of Practice Meeting Schedule 13 – 17 October 2008 Bryn Mawr College MONDAY 13 OCTOBER 07.30 Registration & Welcome Coffee Opens, Thomas Great Hall, Bryn Mawr College InnovationWell Workshop Pre-Conference Workshop: Advances in Information, Communications and Knowledge Management Support Systems in R&D, chaired by John Conway (Accelrys) and Frank Hollinger (Sphaera Pharma), 09.00 – 18.00 [Thomas 110 & Thomas Great Hall] Speaker Presentations and User Perspectives will be used to seed discussions on current and future research needs in Knowledge Management in R&D support systems, which will be carried out using a wiki-supported Knowledge Cafe format. 09.00 Frank Brown (Accelrys), Data is only Valuable if you can Extract the Information 09.30 Chris Culberson (Merck Research Laboratories), WISK: What I Should Know – Mining Chemical Transformations to see What Really Works 10.00 Ralph T. Mosley (Pharmasset), Going Big to Small: What happens when you leave Big Pharma? 10.30 Coffee Break 11.00 Knowledge Cafe on Perspectives [Thomas Great Hall] 12.30 Group Discussion 13.00 Lunch 14.00 Tim McIntyre (GlaxoSmithKline), Workflow Application Enhances Productivity 14.30 Chris Smith (Pfizer), Risk-based Decision Making based on Complex Physical Chemical, Environmental Fate and Toxicological Effect Data Sets for Pharmaceutical Products and their Intermediates 15.00 Barry Hardy (Douglas Connect), Knowledge-Oriented Collaboration in Virtual Organisation Structures 15.30 Coffee Break 16.00 Knowledge Cafe on Perspectives [Thomas Great Hall] 17.30 Group Discussion [Thomas Great Hall] eCheminfo Workshop Virtual Screening Best Practices Workshop, facilitated by Barry Hardy (Douglas Connect), 09.00 – 18.15 [Dalton 300] This wiki-supported Community of Practice Workshop and Forum will discuss and advance best practice in virtual screening and docking, will advance the development of co-created best practices for comparison studies, and will review latest developments in method development and applications related to virtual screening applications in drug discovery. The workshop will use a discussion-based Knowledge Café format with an agenda to: * share experiences on best practices in ligand-based virtual screening * share experiences on best practices in target-based virtual screening * discuss scoring functions and performance of methods * discuss best practices for conducting comparison studies 09.00 Introduction & Overview 09.30 Discussion of practices for ligand-based screening 11.00 Coffee Break 11.30 Discussion of practices for scoring 13.00 Lunch 14.00 Discussion of practices for target-based screening 15.45 Coffee Break 16.15 Discussion of practices for scoring 17.15 Discussion of rules and execution of comparison studies 18.30 Refreshments & Dinner [Wyndham Alumnae House] TUESDAY 14 OCTOBER InnovationWell InterAction Session Systems Biology, chaired by Keith Elliston (Genstruct), 09.00 – 13.00 [Thomas 110] 09.00 Chair’s Introduction & Opening Remarks 09.15 Darius M. Dziuda (Central Connecticut State University), Ensemble Classifiers and Biomarker Discovery 09.45 Frank Tobin (Tobin Consulting), Integrative Mathematical Modeling of Biological Systems 10.15 David S. Lester (Innovative Technologies in Health and Wellness, Inc.), Using a Systems Approach to Determine Diabetic Patient Interventions and Outcomes 10.45 Coffee Break 11.15 Knowledge Cafe Discussion [Thomas Great Hall] 13.00 Lunch eCheminfo InterAction Session Docking & Scoring, chaired by Chaya Duraiswami (GlaxoSmithKline), 09.00 – 13.00 [Dalton 300] 09.00 Chair’s Introduction & Opening Remarks 09.15 John Irwin (UCSF), Retrospective and Prospective Investigation of Docking Performance 09.45 Zsolt Zsoldos (SimBioSys Inc.), The eHiTS Scoring Function 10.15 Johannes H. Voigt (Schering Plough), Cross-docking to CDK2: a Virtual Screening Study 10.45 Coffee Break 11.15 Lance Westerhoff (Quantum Bio), Application of Quantum Mechanical Pairwise Energy Decomposition to Structure-based Drug Design 11.45 Georgia McGaughey (Merck Research Labs), Ligand- and Structure-based methods: Comparison of Methods 12.15 Panel Discussion 13.00 Lunch InnovationWell InterAction Session Computational Biology, chaired by Debraj GuhaThakurta (Rosetta Inpharmatics, Merck & Co.), 14.00 – 18.30 [Thomas 110] 14.00 Chair’s Introduction & Opening Remarks 14.15 Stephen W. Edwards (U.S. Environmental Protection Agency), Systems Biology and Mode of Action Based Risk Assessment 14.45 Paul McDonagh (Gene Network Sciences), Reverse Engineering and Simulating Causal Genetical Genomics Networks 15.15 Christopher M.L.S. Bouton (Blue Tree Consulting), Semantic Web Modeling of Biological Systems 15.45 Coffee Break 16.15 James R. Brown (GlaxoSmithKline), Comparative Genomics and Drug Discovery 16.45 Jake Chen (Indiana University), Translational Bioinformatics: Challenges for New Computational Tools 17.15 Debraj GuhaThakurta (Rosetta Inpharmatics, Merck & Co.), Using Genetics, Gene Expression and Pathway Mining in Pharmaceutical Discovery: Application towards Metabolic and Cardiovascular Disorders 17.45 Panel Discussion eCheminfo InterAction Session Application of MM-PBSA Free Energy Methods in Drug Discovery, chaired by Judith Lalonde (Bryn Mawr College), 14.00 – 18.30 [Dalton 300] 14.00 Chair’s Introduction & Opening Remarks 14.15 Alexey Ornufriev (Virginia Tech), Implicit Solvent Models: Practical Uses, Advantages and Limitations 14.45 David Case (Rutgers University), Scoring and Re-scoring Ligand Binding Energies using Implicit Solvent Models 15.15 Rommie Amaro (UCSD), Comparative Studies using Explicit and Generalized Born Molecular Dynamics Simulations of Influenza Neuraminidases 15.45 Coffee Break 16.15 Peter Coveney (Univ. College London), Rapid and Accurate Determination of Binding Free Energies in Protein-Drug Systems using Automated Workflows across Federated Intercontinental Supercomputing Grids 16.45 Anna Kohlmann (Ariad Pharmaceuticals), Deploying Prime MM-GBSA in Kinase Inhibitor Lead Optimization: from Docking to Local QSAR models 17.15 Scott Brown (Abbott), In what Contexts can we reliably use MM-PBSA in Industrial Drug Discovery? 17.45 Panel Discussion 18.30 Poster Session, Refreshments and Food [Thomas Great Hall] WEDNESDAY 15 OCTOBER InnovationWell InterAction Session Knowledge Management in Translational Medicine, chaired by Barry Hardy (Douglas Connect), 09.00 – 18.00 [Thomas 110] 09.00 Chair’s Introduction & Opening Remarks 09.15 Christopher M.L.S. Bouton (Blue Tree Consulting), Knowledge Engineering in R&D Organizations: Advantages and Considerations 09.45 John Wilbanks (Creative Commons), Breaking down Barriers to Collaboration - the Health Commons Initiative 10.15 Coffee Break 10.45 Barry Bunin (Collaborative Drug Discovery), Community-based Collaborative Drug Discovery for Neglected Infectious Diseases and Cancer 11.15 Michael Liebman (Strategic Medicine, Inc.), Knowledge Management Solutions for Breast Cancer Biomarkers 11.45 Jerry Wright (Johns Hopkins Medical Institutions), Extending the GeneGo Pathway Analysis Platform to Understand Cystic Fibrosis 12.15 Panel Discussion 13.00 Lunch 14.00 Anastasia Christianson (AstraZeneca), Translating Pre-clinical Data to Clinical Outcomes 14.30 James Golden (Accenture), Collecting and Aggregating Open Source Intelligence for Translational Medicine 15.00 John Speakman (National Cancer Institute), The Cancer Biomedical Informatics Grid (caBIG™): Re-engineering the Clinical Trials Enterprise 15.30 Coffee Break 16.00 William Hayes (Biogen Idec), bioPharma Problems that Semantic Web Technologies can solve now 16.30 Andrew McMurry (Harvard Medical School), Using Peer-to-peer Network Systems to obtain Tissue – the Achievements of the Shared Pathology Informatics Network (SPIN) 17.00 Eugene Clark (Partners Healthcare), Supporting Clinical Infrastructure and Processes with a Genetic Knowledge Repository 17.30 Panel Discussion eCheminfo InterAction Session Accurate Calculation of pKas, chaired by Paul Labute (Chemical Computing Group), 09.00 – 13.00 [Dalton 300] 09.00 Chair’s Introduction & Opening Remarks 09.15 Emil Alexov (Clemson University), Modeling Ionization States and Proton Uptake/Release in Receptor-Ligand Association 09.45 Jens Erik Nielsen (University College Dublin, Ireland), Improving the Accuracy of Calculated Protein pKa Values using NMR Spectroscopy 10.15 Francisco Hernandez-Guzman (Accelrys), A Fast and Accurate Computational Approach to Protein Ionization Combining the Generalized Born Model with an Iterative Mobile Cluster Method 10.45 Coffee Break 11.15 Maja Mihajlovic (City College of New York), Calculations of pH-dependent Binding of Peptides to Biological Membranes 11.45 Gernot Kieseritzky (Freie Universitaet Berlin), Improved pKA Prediction: Combining Empirical and Semi-microscopic Methods 12.15 Panel Discussion 13.00 Lunch eCheminfo InterAction Session In Silico-based Chemogenomics, chaired by Fabrice Moriaud (MEDIT), 14.00 – 18.00 [Dalton 300] 14.00 Chair’s Introduction & Opening Remarks 14.15 Michael Keiser (UCSF), Drug Repurposing and Side-effect Elucidation by Statistical Chemical Similarity 14.45 Brian Marsden (University of Oxford), Doing more than just the Structure – Insights into Kinase Structure and Drug Discovery by Structural Genomics 15.15 Joe Eyermann (AstraZeneca), Using Homology Models and Structure-Based Design to Improve the MAO-A Safety Profile of Oxazolidinone Antibacterials 15.45 Coffee Break 16.15 Alex Tropsha (UNC), Cheminformatics Analysis of Polypharmacological Data 16.45 Charles Andrianjara (Laboratoires Pierre Fabre, France), Chemogenomic Space Exploration: Use of MED-SUMO Tools to Analyse Target and Ligand Space of the Kinome 17.15 Panel Discussion 18.30 Poster Session, Refreshments and Food [Thomas Great Hall]

THURSDAY 16 OCTOBER InnovationWell InterAction Session Applications of Metabolomics to Drug Discovery & Development, chaired by Bruce Kristal (Brigham and Women’s Hospital), 09.00 – 13.00 [Thomas 110] 09.00 Chair’s Introduction & Opening Remarks 09.10 Bruce Kristal (Brigham and Women’s Hospital), Diet-based Plasma Metabolomics: Biomarkers for Disease Risk? 09.50 Jeffrey Shuster (Metabolon), Metabolomics to Advance Drug Discovery 10.30 Coffee Break 11.00 Donna Wilson (Thermo Fisher Scientific), Title TBA 11.40 Pierre Beauparlant (Gemin X Pharmaceuticals Inc.), Target Identification Permits Rationale Development of the Prodrug GMX1777 for the Treatment of Melanoma 12.20 Panel Discussion 13.00 Lunch eCheminfo InterAction Session PDB Ligands: Analysing their Structure & Binding Data, chaired by Marc Nicklaus (National Institutes of Health), 08.45 – 18.00 [Dalton 300] 08.45 Chair’s Introduction & Opening Remarks 09.00 John Westbrook (Rutgers), Finding Small Molecules in the Protein Data Bank Archive 09.30 Howard J Feldman (CCG), Using the mmCIF Dictionary for Ligand Correction 10.00 Igor V. Filippov (NCI), A Highly Annotated SD file of all Ligand Occurrences in the PDB 10.30 Coffee Break 11.00 Raul Cachau (ATP, SAIC-Frederick), Chemically Accurate, Ultra-high Resolution X-ray Crystallography, Macromolecular Structure Analysis, and Drug Design 11.30 Vincent T. Moy (University of Miami), Intermolecular Forces of Cell Adhesion Molecules 12.00 Xue Li (University of Florida), The Application of QM/MM Refinement in Protein-Ligand Complexes for Structure-Based Drug Design 12.30 Panel Discussion 13.00 Lunch 14.00 Paul Hawkins (OpenEye), Validation using the RCSB: Good Idea or Bad Idea? 14.30 Yulia Borodina (NCBI), Reproduction of PDB Ligand structures by Conformational Ensembles at Different Energy Thresholds 15.00 Gerhard Wolber (Inte:Ligand, Austria), Structure-focused Pharmacophores for Drug Discovery from Protein-bound Ligands in the PDB 15.30 Coffee Break 16.00 Marc Nicklaus (NIH), High Quantum-chemical Ligand Energies - True Binding Effects or Crystallographic Artifacts? 16.30 James P. Snyder (Emory), What Energy Price Does a Drug Pay To Bind To a Protein Target? 17.00 Panel Discussion Joint InnovationWell-eCheminfo InterAction Session Predictive ADME, chaired by Anthony E. Klon (Locus Pharmaceuticals), 14.00 – 18.00 [Thomas 110] 14.00 Chair’s Introduction & Opening Remarks 14.15 Anton Hopfinger (University of New Mexico), Novel MI-QSAR Descriptors for Use in Modeling Membrane Transport Processes Such as Skin Penetration Enhancement 14.45 Heidi Einolf (Novartis), Predictions of Metabolic Drug Drug Interactions 15.15 Yojiro Sakiyama (Pfizer), Application of Machine Learning Tools for in silico ADME Screening 15.45 Coffee Break 16.15 Olga Obrezanova (BioFocus DPI), Automatic QSAR Modeling of Blood-Brain Barrier Penetration by Gaussian Processes Method 16.45 Anthony E. Klon (Locus Pharmaceuticals), Comparison of Machine Learning Algorithms to Predict ADME Properties Using Diverse Chemical Descriptors and Molecular Fingerprints 17.15 Panel Discussion 18.30 Knowledge Café & Dinner on Collaboration Opportunities in Predictive ADME & Predictive Toxicology [Thomas Great Hall] FRIDAY 17 OCTOBER eCheminfo InterAction Session PDB Ligands: Analysing their Structure & Binding Data, chaired by Marc Nicklaus (National Institutes of Health), 09.00 – 13.00 [Dalton 300] 09.00 Fabrice Moriaud (MEDIT), Exploration of the Chemical Diversity Generated by the Hybridisation of PDB Ligands 09.30 Anne Chaka (NIST), The Need for High Quality PDB Data to Drive Improvement in Ligand Binding Predictions 10.00 Esther Kellenberger (Univ. Strasbourg, France), PDB ligands and Drug Design: Carving out the Compound and its Cavity, and Checking out their Chemistry 10.30 Coffee Break 11.00 Chao-Yie Yang (University of Michigan), The PDBbind Database: Collection of Binding Data of the Complexes in PDB 11.30 Jim Dunbar (University of Michigan), BindingMOAD - Analyzing High Quality PDB Entries with Known Binding Data 12.00 Janna Wehrle (NIGMS), Are we there yet? Expanding the Target-Ligand Structure & Affinity Dataset 12.30 Panel Discussion and Concluding Remarks 13.00 Lunch Joint InnovationWell-eCheminfo InterAction Session Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia), 08.45 – 16.00 [Thomas 110] 08.45 Chair’s Introduction & Opening Remarks 09.00 Alex Tropsha (UNC), Predictive Chemical Toxicity Models using in vitro - in vivo Correlations Enriched by Cheminformatics 09.30 Ann Richard (EPA), EPA DSSTox and ToxCast Project Updates: Generating New Data and Linkages in Support of Public Toxico-Cheminformatics Efforts 10.00 Barry Hardy (Douglas Connect), The OpenTox Predictive Toxicology Framework 10.30 Coffee Break 11.00 Artem Cherkasov (University of British Columbia), The Use of Conventional Drug Design Technologies for Identification of Potential Endocrine Disruptors Interacting with Sex-Hormone Binding Globulin in Zebra Fish 11.30 Weida Tong (FDA), The FDA’s Endocrine Disruptor Knowledge Base (EDKB) – Lessons Learned in QSAR Modeling and Applications 12.30 Lunch 13.30 Curt Breneman (RPI), A Hard Look at Predictive Modeling: How Much Data is Enough? 14.00 Andreas Maunz (Freiburg Center for Data Analysis and Modelling), New Lazar Developments and Data Mining Techniques for the Identification of Structural Alerts 14.30 Panel Discussion 16.00 Close of Program