THURSDAY, October 28

   7:30 Continental breakfast
   8:15 Welcome - Organizers
Session chair: Dill
   8:30 Sternberg, Protein function prediction using protein interaction information
   9:00 Nussinov, Multi scale combinatorial docking of the proteome for functional
   9:30 Olson, Automated visualization of sub-cellular molecular environments
  10:00 Coffee break
  10:30 Lichtarge, Evolution - a guide to biological function and redesign
  11:00 Dunbrack, Homologous protein-protein interfaces observed in multiple
                                crystal forms
  11:30 Zhou, H-X, Automated prediction of protein-protein association rate constants
  12:00 Lunch
Session chair: Nussinov
   1:30 Wodak, Blind predictions of protein interfaces by docking calculations in CAPRI
   2:00 Janin, Benchmarking the affinities of protein-protein complexes
   2:30 Moult, Genetic variants in common human disease
   3:00 Coffee break
   3:30 Dill, Towards an improved computational model of aqueous solvation
   4:00 Elber, On the design of docking potentials
   4:30 Bajaj, Faster energetics, forces, interfaces for multi-protein complexes
   5:00 Free time, dinner on your own
Poster session
   8:00 - 10:00 Poster presentations, open bar

FRIDAY, October 29

   7:30 Continental breakfast
Session chair: Lichtarge
   8:30 Voth, Systematic multiscale simulation of multiprotein complexes
   9:00 Jernigan, Assembling protein machines and seeking their functions
   9:30 Bonvin, Building macromolecular assemblies by information-driven docking.
                                   Challenges and perspectives
  10:00 Coffee break
  10:30 Cowburn, Some new NMR approaches to protein-protein interactions
  11:00 Uetz, Mapping protein interactions using improved yeast two-hybrid screens
                        and other methods
  11:30 Washburn, Combinatorial depletion analysis to assemble the network
                                  architecture of chromatin remodeling complexes
  12:00 Lunch
Session chair: Sternberg
   1:30 Joachimiak, Human microbiome - the next structural frontier
   2:00 Godzik, The unexplored interactome - host-commensal bacteria interactions
   2:30 Fetrow, Clustering functionally relevant space at the molecular level:
                            subfamily classification and functional mechanism in the peroxiredoxin
                            protein family
   3:00 Coffee break
   3:30 Aloy, Interactome 3D: pushing structural details into protein interaction networks
   4:00 Vajda, Reducing the complexity of protein docking
   4:30 Vakser, Protein docking methodology for structural genomics
   6:30 Reception and 7:00 - 9:00 Dinner at Eldridge

SATURDAY, October 30

   7:30 Continental breakfast
Session chair: Dunbrack
   8:30 Ma, Miltiscale simulation and refinement of protein structure and folding
   9:00 Brooks, Exploring pH dependent protein-protein interactions in an energy
                            independent chaperone
   9:30 Marshall, PHOENIX: A scoring function for affinity prediction derived using
                              high-resolution crystal structures and thermodynamic measurements
  10:00 Coffee break
  10:30 Weng, ZRANK 3.0: combining atom-based and residue-based scoring functions
                          for protein-protein docking
  11:00 Camacho, The phase diagram of protein interactions: What physical properties
                                can tell us about biological function
  11:30 Liang, Predicting structures and protein-protein interactions of beta-barrel
                          membrane proteins from sequences
  12:00 Lunch
Session chair: Brooks
   1:30 Fernandez-Recio, Integration of full-atom docking energy into coarse-grained
                                            molecular mechanics for multi-scale simulations of protein-
                                            protein association
   2:00 Zhou, Y, Template-based prediction of RNA-binding domains and RNA-binding
                              sites and application to structural genomics targets
   2:00 Karanicolas, Small-molecule modulation of protein interactions
   3:00 Coffee break
   3:30 Deeds, The dynamic of assembly in protein interaction networks
   4:00 Kozakov, Global sampling of macromolecular recognition landscapes using
                               Fast Fourier Transform and their generalizations
   4:30 Ruvinsky, Equilibrium fluctuations and structural instabilities in proteins
   4:45 Kundrotas, GWIDD: Genome-wide structural modeling of protein-protein
   5:00 Concluding remarks - Vakser, Vajda