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

                                predictions

   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

   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

   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

                                  interactions

   5:00 Concluding remarks - Vakser, Vajda