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

                            complexes

   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

                              models

   5:15 Free time, dinner on your own

Poster session

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

   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

   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

                            crystals

  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

                                    optimization

  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

                           complexes

   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