Workshop I: Design of Drugs and Chemicals that Influence Biology - IPAM

Workshop I: Design of Drugs and Chemicals that Influence Biology

Part of the Long Program Navigating Chemical Compound Space for Materials and Bio Design
April 4 - 8, 2011

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, April 4, 2011

Morning Session

08:00-09:00
Check-In/Light Breakfast (Hosted by IPAM)
09:00-09:15
Welcome and Opening Remarks
09:15-10:45
William Jorgensen (Yale University)
Overview of Computer-Aided Drug Discovery
10:45-11:15
Break
11:15-12:05
Ursula Roethlisberger (École Polytechnique Fédérale de Lausanne (EPFL))
Integrating Computational Methods to Retrofit Enzymes to Synthetic Pathways

Afternoon Session

12:15-14:00
Lunch (on your own)
14:00-14:50
Rich Friesner (Columbia University)
Incorporating the Effects of Water Structure, Ligand Strain, and Protein Reorganization into the Prediction of Protein-Ligand Binding Affinity
15:00-15:30
Lightning Poster Presentations
15:30-16:00
Break
16:00-16:50
Charles Brooks (University of Michigan)
Methods and molecules for interrogation and control of biological processes
17:00-19:00
Reception and Poster Session (Hosted by IPAM)

Tuesday, April 5, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Dimitris Agrafiotis (Johnson & Johnson Pharmaceutical Research & Development, LLC)
Self-organizing algorithms in data mining and computational drug design
10:00-10:15
Break
10:15-11:05
Anastassia Alexandrova (University of California, Los Angeles (UCLA))
Multi-scale approaches in description and design of enzymes
11:15-11:30
Break
11:30-12:20
Maria Ramos (University of Porto)
Computational Enzymology and Drug Design

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Jiali Gao (University of Minnesota, Twin Cities)
Quantum Mechanical Approaches to Biomolecular Simulations: From a Single Electron to Fully Solvated Proteins
15:30-16:00
Break
16:00-16:50
Robert Rizzo (SUNY Stony Brook)
Molecular Dynamics and Docking Approaches to Characterize Drug Resistance and Assist Lead Discovery

Wednesday, April 6, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Brian Kuhlman (University of North Carolina)
Computational Design of Protein Structures and Interfaces
10:00-10:15
Break
10:15-11:05
Amy Keating (Massachusetts Institute of Technology)
Modeling and Designing Protein-Protein Interaction Specificity
11:15-11:30
Break
11:30-12:20
Elisa Fadda (National University of Ireland, Galway)
Quantifying the standard binding free energy of highly conserved water molecules in proteins binding sites: how important is the choice of water model?

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Kendall Houk (University of California, Los Angeles (UCLA))
Design of Enzymes for Non-natural Reactions
15:30-16:00
Break
16:00-16:50
William Jorgensen (Yale University)
Recent Progress on Discovery of Drug Candidates

Thursday, April 7, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Cecilia Clementi (Freie Universität Berlin)
Prediction of protein functional states by multi-resolution protein modeling
10:00-10:15
Break
10:15-11:05
Jeffery Saven (University of Pennsylvania)
Engineering structure and function with theoretical protein design
11:15-11:30
Break
11:30-12:20
William DeGrado (University of Pennsylvania)
De novo protein design

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Robert Glen (University of Cambridge)
Drug discovery: a multi-objective optimization problem
15:30-16:00
Break
16:00-16:50
Gagerin Papoian (University of Maryland)
Exploring Protein Energy Landscapes with Simulations: Applications to Histone Tails and Allosteric Transitions

Friday, April 8, 2011

Morning Session

08:00-09:00
Continental Breakfast
09:00-09:50
Michele Parrinello (ETH Zurich)
Well-tempered metadynamics: theory and applications
10:00-10:15
Break
10:15-11:05
Shaomeng Wang (University of Michigan)
Design of small-molecule drugs to target protein-protein interactions in the apoptosis pathways
11:15-11:30
Break
11:30-12:20
Alexandre Tkatchenko (University of Luxembourg)
Weak van der Waals interactions: How well can we treat them and how relevant are they for peptides and proteins?

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:20
Andrej Sali (University of California, San Francisco (UCSF))
Virtual Ligand Screening Against Comparative Protein Structure Models
15:30-16:00
Break
16:00-16:50
Parag Mallick (Stanford University)
Title not available
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