Sunday, September 30


7:30 Continental breakfast

8:15 Welcome Organizers

Interactions, Structure, Function 1

Session chair: Honig

8:30 Sternberg, Computational studies on the function and activity of biomolecules

9:00 Godzik, Structural Genomics meets Systems Biology after 7 years of PSI we know the molecular face of central metabolism in bacteria

9:30 Lichtarge, Protein interactions: Towards rules and regulation

10:00 Coffee break

10:30 Nussinov, Modeling protein interactions: What is the preferred way for proteins to interact?

11:00 Moult, Genetic variations in protein interfaces

11:30 Marshall, Chimeric proteins and enzyme dynamics - the role of entropy

12:00 Lunch

Docking and Binding

Session chair: Sternberg

1:30 Abagyan, Induced fit in molecular interactions

2:00 Weng, Protein-protein docking and design with ZRANK

2:30 Ritchie/Kozakov, Practical 5D FFT docking

3:00 Coffee break

3:30 Wodak, Mechanism of 3D domain swapping in proteins

4:00 Shen/Vajda, Docking refinement by Semidefinite Underestimation

4:30 Zhou, Toward building structural models for multi-component protein-DNA complexes

5:00 Free time, dinner on your own

Poster session

8:00-10:00 Poster presentations, open bar


monday, October 1


7:30 Continental breakfast

Experimental and Computational Determination of Complexes

Session chair: Cowburn

8:30 Sali, Determining the structures of macromolecular assemblies

9:00 Chiu, Cryo-EM based modeling of molecular machine

9:30 Aloy, Protein interaction specificity: Using 3D structures to unveil compensatory effects in protein interaction networks

10:00 Coffee break

10:30 Cowburn, What do experimentalists want (and what can they do)?

11:00 Joachimiak, Bridging structural biology and genomics

11:30 Uetz, Protein-protein interactions in bacteria: from sequence to structure

12:00 Lunch

Session chair: Sali

1:30 Chance, Merging computational and experimental data in structural mass spectrometry experiments

2:00 Washburn, Visualizing protein complexes and protein interaction networks with normalized spectral abundance factors

2:30 Dunbrack, Identifying biological interfaces in protein crystal structures

3:00 Coffee break

Discussion: Protein Complex Initiative


6:30 Reception and Dinner at Liberty Hall


tuesday, October 2


7:30 Continental breakfast

Interactions, Structure, Function 2

Session chair: Merz

8:30 Gronenborn, NMR approaches to map protein-protein interactions: Methods and applications

9:00 Honig, Using structural alignments to identify remote functional relationships between proteins: Should the fold-based classifications of proteins be abandoned

9:30 Skolnick, Prediction and refinement of protein complexes

10:00 Coffee break

Session chair: Skolnick

10:30 Kortemme, Design of selective and multi-specific protein interfaces

11:00 Camacho, Insights on protein disorder, foldability and binding

11:30 Merz, Quantum Mechanics in Structural Biology

12:00 Lunch

Session chair: Uetz

1:30 Verkhivker, Protein folding and binding in signal transduction networks: From simulations of disordered proteins to drug discovery of cancer therapeutics

2:00 Zhang, New approaches to protein structure prediction

2:30 Coffee break

3:00 Vakser, Multiscale approach to protein interactions

3:30 Murray, Membrane matters: Membrane mediated protein-protein interactions

4:00 Im, Understanding of helix-lipid and helix-helix interactions in membranes

4:30 Concluding remarks Vakser, Vajda

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