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Program and Schedule
| | eCheminfo InterAction Meeting at Bryn Mawr, Philadelphia (13-17 October 2008) | Program Agenda and Schedule
MONDAY 13 OCTOBER
07.30 Registration & Welcome Coffee Opens, Thomas Great Hall, Bryn Mawr College
Virtual Screening Best Practices Workshop, facilitated by Barry Hardy (Douglas Connect), 09.00 – 18.15 [Dalton 300]
More Information on Workshop....
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
Docking & Scoring, chaired by Chaya Duraiswami (GlaxoSmithKline), 09.00 – 13.00 [Dalton 300]
More Information on Session including Abstracts and Biographies....
09.00 Chair’s Introduction & Opening Remarks
09.15 John Irwin (UCSF), Retrospective and Prospective tests with Docking
09.45 Georgia McGaughey (Merck), Ligand- and Structure-based methods: Comparison of Methods
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 Zsolt Zsoldos (SimBioSys Inc.), The eHiTS Scoring Function
12.15 Panel Discussion
13.00 Lunch
Application of MM-PBSA Free Energy Methods in Drug Discovery, chaired by Judith Lalonde (Bryn Mawr College), 14.00 – 18.30 [Dalton 300]
More Information on Session including Abstracts and Biographies....
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
Accurate Calculation of pKas, chaired by Paul Labute (Chemical Computing Group), 09.00 – 13.00 [Dalton 300]
More Information on Session including Abstracts and Biographies....
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 Matthew Davies (Jenner Institute, UK), Benchmarking Protein pKa Predictions
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
In Silico-based Chemogenomics, chaired by Fabrice Moriaud (MEDIT), 14.00 – 18.00 [Dalton 300]
More Information on Session including Abstracts and Biographies....
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 Alex Tropsha (UNC), Cheminformatics Analysis of Polypharmacological Data
15.45 Coffee Break
16.15 Charles Andrianjara (Laboratoires Pierre Fabre, France), Chemogenomic Space Exploration: Use of MED-SUMO Tools to Analyse Target and Ligand Space of the Kinome
16.45 Speaker & Title TBA
17.15 Panel Discussion
18.30 Poster Session, Refreshments and Food [Thomas Great Hall]
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THURSDAY 16 OCTOBER
PDB Ligands: Analysing their Structure & Binding Data, chaired by Marc Nicklaus (National Institutes of Health), 08.45 – 18.00 [Dalton 300]
More Information on Session including Abstracts and Biographies....
08.45 Chair’s Introduction & Opening Remarks
09.00 John Westbrook (Rutgers), Finding Small Molecules in the Protein Data Bank
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 Lance Westerhoff (QuantumBio), 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), How Much Energy Does a Small Molecule Pay to Bind to a Protein?
17.00 Panel Discussion
Predictive ADME, chaired by Anthony E. Klon (Pharmacopeia Drug Discovery), 14.00 – 18.00 [Thomas 110]
More Information on Session including Abstracts and Biographies....
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 (Pharmacopeia), Comparison of Machine Learning Algorithms to Predict ADME
17.15 Panel Discussion
18.30 Knowledge Café & Dinner on Collaboration Opportunities in Predictive ADME & Predictive Toxicology [Thomas Great Hall]
FRIDAY 17 OCTOBER
PDB Ligands: Analysing their Structure & Binding Data, chaired by Marc Nicklaus (National Institutes of Health), 09.00 – 13.00 [Dalton 300]
More Information on Session including Abstracts and Biographies....
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), High Throughput Fingerprinting of Ligand-Protein Interactions
10.30 Coffee Break
11.00 Renxiao Wang (SIOC, Shanghai, PR China), 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
Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia), 08.45 – 16.00 [Thomas 110]
More Information on Session including Abstracts and Biographies....
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 Richards (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
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