Workshop II: Optimization, Search and Graph-Theoretical Algorithms for Chemical Compound Space - IPAM

Workshop II: Optimization, Search and Graph-Theoretical Algorithms for Chemical Compound Space

Part of the Long Program Navigating Chemical Compound Space for Materials and Bio Design
April 11 - 15, 2011

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, April 11, 2011

Morning Session

08:00-09:00
Check-In/Light Breakfast (Hosted by IPAM)
09:00-09:50
Jean-Loup Faulon (Université d'Évry-Val d'Essonne)
Local Enumeration of the Chemical Space with Circular Fingerprints
10:00-10:15
Break
10:15-11:05
John Irwin (University of California, San Francisco (UCSF))
Predicting Off-targets for Approved Drugs
11:15-11:30
Break
11:30-12:20
Jack Snoeyink (University of North Carolina)
Scientific Benchmarks for Structure Prediction Code

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Klaus-Robert Müller (Technische Universität Berlin)
Predicting Properties of Small Molecules with Kernel-Based Machine Learning Methods
15:30-16:00
Break
16:00-16:50
Farhad Hormozdiari (University of Washington)
Extended Nearest Neighbor Classification Methods for Predicting Small Molecule Activity
17:00-19:00
Reception and Poster Session (Hosted by IPAM)

Tuesday, April 12, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
David Wales (University of Cambridge)
Exploring Energy Landscapes: From Molecules to Nanodevices
10:00-10:15
Break
10:15-11:05
Mark Tuckerman (New York University)
Generating Free Energy Landscapes: From Solvation to Biomolecules and Crystalline Polymorphs
11:15-11:30
Break
11:30-12:20
Mauro Maggioni (Johns Hopkins University)
Geometric Analysis of Molecular Dynamics Data, Diffusion Geometry and Reaction Coordinates

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Mike McKerns (California Institute of Technology)
A Massively-Parallel Heterogeneous Computing Framework for Optimization and Rigorous Parameter Sensitivity Analysis
15:30-16:00
Break
16:00-16:50
Shawn Martin (Sandia National Laboratories)
Topology of Cyclo-Octane Energy Landscape

Wednesday, April 13, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
William Hart (Sandia National Laboratories)
Rethinking Optimization Challenges for Molecular Docking Applications
10:00-10:15
Break
10:15-11:05
Venkat Venkatasubramanian (Purdue University)
Molecular Products Design: Challenges and Opportunities
11:15-11:30
Break
11:30-12:20
Rolf Backofen (Albert-Ludwigs-Universität Freiburg)
The Tedious Task of Finding Common RNA Sequence Structure Properties

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Danail Bonchev (Virginia Commonwealth University)
Substructures and Patterns in 2-D Chemical Space
15:30-16:00
Break
16:00-16:50
Pierre Baldi (University of California, Irvine (UCI))
Algorithms and Data Structures for Efficiently Storing, Compressing, Retrieving, and Scoring Small Molecules in Chemical Space

Thursday, April 14, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Jean-Louis Reymond (Universität Bern)
Enumeration, Mapping and Scoring of Chemical Space for Drug Discovery
10:00-10:15
Break
10:15-11:05
Tamon Stephen (Simon Fraser University)
Two pairs of boolean functions in biology
11:15-11:30
Break
11:30-12:20
Berend Rinderspacher (Army Research Laboratory)
Molecular Optimization Using Nuclear Charge Distributions

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Artem Cherkasov (University of British Columbia)
Prediction of Highly-Connected 'Hub'-Proteins in Protein Interaction Networks Using Conventional Molecular QSAR
15:30-16:00
Break
16:00-16:50
Markus Meringer (Deutsche Forschungsanstalt für Luft- und Raumfahrt eV (DLR))
Generation of Molecular Graphs and Applications in Chemistry

Friday, April 15, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Wei Wang (University of North Carolina)
Discriminative Structural Motif Mining for Protein Classification
10:00-10:15
Break
10:15-11:05
Tatsuya Akutsu (Kyoto University)
Inference and Enumeration of Chemical Structures from Feature Vectors
11:15-11:30
Break
11:30-12:20
Kyle Camarda (University of Kansas)
An Optimization-Based Method for the Design of Novel Molecular Systems

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Panel Discussion
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