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Ravindra
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Program and Schedule
| | eCheminfo InterAction Meeting at Bryn Mawr, Philadelphia (12-16 October 2009) |
Program Agenda and Schedule
MONDAY 12 OCTOBER
07.30 Registration & Welcome Coffee Opens, Thomas Great Hall, Bryn Mawr College
Drug Binding Affinities Workshop, Co-chaired by Scott Brown (Abbott Laboratories), Zheng Yang (GlaxoSmithKline Pharmaceuticals), Ruhong Zhou (IBM) and Judith Lalonde (Bryn Mawr College)
More Information on Workshop Activities....
[Dalton room 300]
9:00 Welcome and Overview, Judith LaLonde (Bryn Mawr College)
9:15 Background and Overview on MM, Ruhong Zhou (IBM)
9:30 Break-out Discussions on MM
10:00 Background and Overview on Solvation Models, Scott Brown (Abbott Laboratories)
10:15 Break-out Discussions on Solvation Models
11:00 Coffee Break
11:30 Background and Overview on Surface Area, Judith LaLonde (Bryn Mawr College)
11:45 Break-out Discussions on Surface Area
13:00 Lunch
14:00 Case Studies Introduction, Zheng Yang (GlaxoSmithKline Pharmaceuticals)
14:05 Dong Xu (University of California, San Diego), MM-GBSA-based Calculation of Binding Energies of Hemagglutinin-glycan interactions involved in Avian Flu Virus Infection Initiation
15:00 Scott Brown (Abbott Laboratories), MM-PBSA as a Tool for Prospective Drug-Discovery Research
15:45 Coffee Break
16:15 Natasja Brooijmans (Wyeth Research), Docking and MM/GBSA Re-scoring in Lead Identification
17:00 Round Table Discussion, Zheng Yang (GlaxoSmithKline Pharmaceuticals)
18.30 Refreshments & Dinner [Wyndham Alumnae House]
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TUESDAY 13 OCTOBER
Structure-Based Drug Design, Chaired by Alan Cheng (Amgen)
More Information on Session including Abstracts and Biographies....
[Dalton room 300]
08.30 Chair’s Introduction & Opening Remarks
08.45 Maxwell D. Cummings (Tibotec), Binding of the HCV NS3/4A Protease Inhibitor TMC435 to its Viral Target Enzyme
09.10 Robert Abel (Schrodinger), The Role of Solvent in Protein-Ligand Binding – a WaterMap Centric View
09.35 Ernesto Friere (Johns Hopkins University), The Role of Thermodynamics and Calorimetry in the Optimization of Drug Candidates
10.00 Coffee Break
10.30 Gergely Toth, Towards the Significance of Unconventional Hydrogen Bonds in Structure Based Drug Design
10.55 Pu Liu (Johnson & Johnson PR&D), A Self-organising Algorithm for Modeling Protein Loops
11.20 Arnout Voet (KU Leuven), Discovery of HIV-1 IN – LEDGF/p75 Interaction Inhibitors using a Virtual Screening Approach
11.45 Zhuyan Guo (Schering-Plough), Structure-Based Drug Discovery of Inhibitors of TNF-alpha Converting Enzyme (TACE)
12.10 Panel Discussion
13.00 Lunch
Macromolecular Interactions and Networks, Chaired by Emil Alexov (Clemson University)
More Information on Session including Abstracts and Biographies....
[Dalton room 300]
14.00 Chair’s Introduction & Opening Remarks
14.15 Alex Morozov (Rutgers University), Evolutionary Origin of Pairwise and Higher-order Correlations among Drug-resistance Mutations in HIV-1 Subtype B Protease
14.40 Anna Panchenko (National Center for Biotechnology Information), Role of Intrinsic Disorder in Protein-Protein Interactions
15.05 Marcia Fenley (Florida State University), Revisiting the Binding Energetics of Charged Ligand-Nucleic Acid Complexes using Novel Nonlinear and Modified Poisson-Boltzmann Solvers
15.30 Coffee Break
16.00 Amos Fatokun (John Hopkins), Molecular Mechanisms of (Neuronal) Cell Death: Convergence or Divergence of Multiple Pathways?
16.25 Eric Hajjar (Universita degli Studi di Cagliari and Sardinian Laboratory for Computational Materials Science), Towards Design of Antibiotics with Improved Permeation Properties through Bacterial Pores
16.50 Rameshwar Kadam (University of Berne), Modeling Protein-Carbohydrate Recognition: a Study of Glycopeptide Dendrimer Ligands of the Fucose Binding Lectin PA-IIL from Pseudomonas aeruginosa
17.15 Panel Discussion
18.30 Poster Session, Refreshments and Food [Thomas Great Hall]
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WEDNESDAY 14 OCTOBER
Structure-Based Drug Design, Chaired by Natasja Brooijmans (Wyeth)
More Information on Session including Abstracts and Biographies....
[Dalton room 300]
09.00 Chair’s Introduction & Opening Remarks
09.15 Ian Craig (Novartis), Does Ensemble Docking Improve Virtual Screening Enrichment?
09.45 Zsolt Zsoldos (SimBioSys), Improving Molecular Docking Through a Tunable Scoring Function
10.15 Jens Meiler (Vanderbilt University), Directed Screening of Glutamate Response Potentiators
10.45 Coffee Break
11.15 Jorg Bentzien (Boehringer Ingelheim), Molecular Modeling towards Potent and Selective Interleukin-2 inducible T-cell Kinase (ITK) Inhibitors
11.45 Devleena Shivakumar (Schrodinger), Practical Application of Free Energy Perturbation Calculations in Drug Discovery
12.15 Panel Discussion
13.00 Lunch
Data Analysis and Visualisation Applications in Chemical Biology
Chaired by Brian Marsden (Structural Genomics Consortium, University of Oxford)
More Information on Session including Abstracts and Biographies....
[Dalton room 300]
14.00 Chair's Introduction & Opening Remarks
14.15 Dimitris Agrafiotis (Johnson & Johnson PR&D), Chemocentric
Visualization of Large, Multidimensional Data in ABCD and 3DX
14.45 Ajit Jadhav (National Chemical Genomics Center), An Open Source
Cheminformatics System for Large-Scale HTS Data Analysis and Visualization
15.15 Wen Hwa Lee (Structural Genomics Consortium Oxford), Structural
and Chemical Biology Data Dissemination for the Masses
15.45 Coffee Break
16.15 Bob Hanson (St. Olaf College), Data Mining and Molecular
Visualisation in Drug Discovery
16.45 Warren DeLano (DeLano Scientific LLC), PyMOL: An Open-Source
Visualization Tool for Chemistry and Biology
17.15 Panel Discussion
18.30 Poster Session, Refreshments and Food [Thomas Great Hall]
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THURSDAY 15 OCTOBER
PDB Ligands, Chaired by John Westbrook (RCSB, Protein Data Bank, Rutgers University) More Information on Session including Abstracts and Biographies....
[Dalton room 300]
09.00 Chair’s Introduction & Opening Remarks
09.15 Kim Henrick, (PDBe, European Bioinformatics Institute), The PDB and Antibiotic Peptide Sequence-like Compounds
09.45 Gerard J. Kleywegt (Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Cambridge), Thoughts about Ligand-Structure Validation
10.15 Howard Feldman (Chemical Computing Group), Ligand Pocket Detection in Biological Assemblies
10.45 Coffee Break
11:15 Nigel W. Moriarty (Lawrence Berkeley National Laboratory), electronic Ligand Builder and Optimisation Workbench (eLBOW): A tool for Ligand Coordinate and Restraint Generation
11:45 Marc Nicklaus (National Institutes of Health), Ligand Energies Calculated Quantum-Chemically in Vacuum and Solvent Model
12.15 Panel Discussion
12.45 Lunch
13.45 Gregory L Warren (OpenEye Scientific Software), Iridium: Marginally Less Bad than the Rest
14.15 Valery Tkachenko (Royal Society of Chemistry), Enabling the World of Internet Based Chemistry Through ChemSpider
14.45 Paul Hawkins (OpenEye Scientific Software), Conformer Generation: Finding and Learning from Failures
15.15 François Delfaud (MEDIT), Mitotic Kinesin Eg5 Inhibitors Generation By Computational MED-Portion Based Drug Design at PDB Scale
15.45 Panel Discussion
16.15 Coffee Break
Predictive Toxicology: Combining in vitro and in silico Techniques in Predictive Toxicology Applications, Co-chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences)
More Information on Session including Abstracts and Biographies....
[Thomas room 110]
09.00 Chair’s Introduction & Opening Remarks
09.15 Richard Judson (US EPA), High Throughput Screening of Toxicity Pathways Perturbed by Environmental Chemicals
09.40 Ellen Berg (BioSeek), Defining Chemical Target and Pathway Toxicity Mechanisms with Primary Human Cell Systems
10.05 Peter Elkin (Mount Sinai School of Medicine, New York), TBA
10.30 Coffee Break
11.00 Barry Hardy (Douglas Connect), Integrated Predictive Toxicology Application Development
11.25 Sanji Bhal (ACD/Labs), Applications of GALAS Modeling Methodology for the Prediction of Drug Safety Related Properties. Evaluation and Expansion of the Model Applicability Domain
11.50 Christodoulos Floudas (Princeton University), Predicting in vivo Toxicities using Optimal Methods for Re-ordering and Logistic Regression
12.15 Panel Discussion
13.00 Lunch
14.00 Kyoung Tai No (Yonsei University), In Silico Prediction of Drug Metabolism in the Liver
14.25 Robert Fraczkiewicz (Simulations Plus), Modeling Rat Liver Toxicity Signature Using Machine Learning Techniques
14.50 Stephen Bryant (NIH), Toxicology Data Sets in PubChem
15.15 Panel Discussion
15:45 Coffee Break
16.15 Knowledge Cafe [Thomas Great Hall]
18.30 Refreshments and Food [Thomas Great Hall]
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FRIDAY 16 OCTOBER
Predictive Toxicology: Combining in vitro and in silico Techniques in Predictive Toxicology Applications, Co-chaired by Richard Judson (US EPA) and Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences)
More Information on Session including Abstracts and Biographies....
[Thomas room 110]
09.00 Chair’s Introduction & Opening Remarks
09.15 Vladimir Poroikov (Institute of Biomedical Chemistry of Russian Academy of Medical Sciences), QSAR Modeling of Toxicity: Comparison of Pharmaceutical and Industrial Chemicals
09.40 Fangping Mu (Los Alamos National Laboratory), Computational Xenobiotics Metabolism Prediction System
10.05 Katya Tsaioun (Apredica), In vitro Models that Predict Major Known Mechanisms of Human Toxicity. Validation, Case Studies and Path Forward
10.30 Coffee Break
11.00 Grace Patlewicz (DuPont), Read-across – a Data Gap Filling Technique – Help or Hindrance? A Practical Perspective
11.25 Michael Pelekis (Simulations Plus), Not Just 'If' or 'Where', but Also 'How Fast' – Predictive Modeling of Kinetic Constants for CYP-Mediated Metabolism
11.50 Anil Aswani (University of California at Berkeley), A Network-Level Approach to Predictive Toxicology
12.15 Panel Discussion
13.00 Lunch
Close of Program
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