THURSDAY, November 8

   7:30 Continental breakfast
   8:15 Welcome - Organizers
Session chair: Sternberg
   8:30 Scheraga, Protein-protein reactions in an important biological process
   9:00 Dill, SEA Water: a better way to handle water in protein simulations
   9:30 Olson, Building and visualizing the Molecular Cell
  10:00 Wodak, Homodimer formation enables new protein function by altering
                            backbone flexibility properties
  10:30 Coffee break
Session chair: Nussinov
  10:45 Dunbrack, Biological dimers of protein kinases in crystals:
                                autophosphorylation, inhibition, and activation
  11:15 Jernigan Extracting dynamics information from multiple structures
  11:45 Lichtarge, What evolution tells us about function and its perturbations
  12:15 Lunch
Session chair: Honig
   1:30 Zhou, Rate constants and mechanisms of intrinsically disordered proteins
                          binding to structured targets
   2:00 Bajaj, Multi-protein docking
   2:30 Weng, Computational docking and design
   3:00 Bonvin, A global surface model for the binding affinity of protein-protein
   3:30 Coffee break
Session chair: Skolnick
   3:45 Elber, Learning to score protein-protein complexes: atomic and residue
                          based potentials
   4:15 Vajda, Docking and scoring: marriage made in heaven
   4:45 Keating, Large experimental datasets for benchmarking protein interaction
   5:15 Free time, dinner on your own
Poster session
   8:00 - 10:00 Poster presentations, open bar

FRIDAY, November 9

   7:30 Continental breakfast
Session chair: Dill
   8:30 Honig, Structure-based prediction of protein-protein interactions
                          on a genome-wide scale
   9:00 Nussinov, Structural networks of signaling pathways on the cellular scale
   9:30 Sternberg, Computational studies on nsSNPs and the interactome
  10:00 Skolnick, On the interplay of physics and evolution in dictating protein structure
                                and function
  10:30 Coffee break
Session chair: Lichtarge
  10:45 Vakser, Comparative docking
  11:15 Moult, Some cogitations on CASP
  11:45 Godzik, From protein-protein to domain-domain interaction networks with
                            (sometimes) structural genomics
  12:15 Lunch
Session chair: Jernigan
   1:30 Brooks, Exploring and modulating protein-protein interactions using salt,
                            pH and small molecules
   2:00 Marshall, The devil's still in the details: electrostatics and entropy
   2:30 Im, Toward glycan structure modeling
   3:00 Coffee break
Session chair: Weng
   3:15 Ma, Enhanced sampling and folding of protein in explicit solvent
   3:45 Liang, Signatures of protein binding surfaces: from structures and predictions
   4:15 DISCUSSION, Future of PPI modeling
   6:30 Reception and 7:00 - 9:00 Dinner at Eldridge

SATURDAY, November 10

   7:30 Continental breakfast
Session chair: Brooks
   8:30 Kuhlman, Using anchoring motifs for the computational design of protein-
                                protein interactions
   9:00 Kortemme, Molecular design - shaping protein conformations and predicting
                                  functional sequences
   9:30 Yeates, Using protein interactions to design novel assemblies: from cages to
  10:00 Grishin, MPI to guide experimental design
  10:30 Coffee break
Session chair: Marshall
  10:45 Camacho, AnchorQuery: Interactive and efficient discovery tool of small
                                molecule protein-protein interaction antagonists
  11:15 Carlson, Mapping protein surfaces with mixed-solvent MD
  11:45 Karanicolas, Identifying inhibitors of protein interactions using pocket
  12:15 Lunch
Session chair: Camacho
   1:30 Furman, Structure-based prediction of peptide binding specificity
   2:00 Mitchell, Structure-based predictive models for mutagenesis effects
   2:30 Bradley, Using symmetry to predict the structures of protein-nucleic
                              acid complexes
   3:00 Coffee break
Session chair: Zhou
   3:15 Deeds, Effective MAP kinase signaling via heterogeneous ensembles of protein
   3:45 Kozakov, Identification of binding and allosteric sites in proteins using
                              FFT sampling, with near experimental accuracy
   4:15 Kundrotas, DOCKGROUND and GWIDD: comprehensive resources for
                                 structural studies of PPI
   4:45 Concluding remarks - Vakser, Vajda