Sunday, June 26

docking and binding


   7:30 Continental breakfast

   8:40 Welcome – Organizers, KU Administration

        Session chair: Sternberg

   9:00 Olson, Visualizing large biomolecular complexes

   9:30 Honig, How to achieve high specificity with low affinity binding: Lessons from the cadherin family of cell-adhesion proteins

  10:00 Nussinov, Modeling interactions in large multimolecular assemblies and in protein molecules by combinatorial docking

  10:30 Coffee break

  11:00 Abagyan, Structural patterns and the specificity of recognition

  11:30 Gray, “Truly blind” docking of a novel anti-cancer therapeutic antibody to the epidermal growth factor receptor

  12:00 Lunch

        Session chair: Olson

   1:30 Weng, Structure, function and evolution of transient and obligate protein-protein interactions

   2:00 Camacho, Everything you need to know but are afraid to ask about scoring functions of protein complexes

   2:30 Ten Eyck, TBA

   3:00 Coffee break

   3:30 Janin, Structural patterns in specific recognition

   4:00 Vajda, Cluster selection and in-cluster refinement for discrimination in protein-protein docking

   4:30 Free time, dinner on your own



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


monday, June 27

interactome, structure-function, Energetics


   7:30 Continental breakfast

        Session chair: Janin

   8:30 Skolnick, Prediction of protein structure, function and druggability on a proteomic scale

   9:00 Washburn, Qualitative and quantitative proteomic analysis via MudPIT

   9:30 Frishman, A domain interaction map based on phylogenetic profiling

  10:00 Coffee break

  10:30 Sternberg, Protein Phenetics - Function, Classification and Interactions

  11:00 Aloy, A structural perspective on protein interactions and complexes

  11:30 Liang, Inferring protein function by local surface matching and similarity assessment

  12:00 Lunch

        Session chair: Nussinov

   1:30 Godzik, Protein interaction networks and disease

   2:00 Marshall, Control of entropy: The key to protein engineering

   2:30 Valencia, TBA

   3:00 Coffee break



   3:30 Wodak, Protein-protein docking procedures: Lessons learned from CAPRI

   4:00-5:30 Future of Protein Interaction Modeling

   6:15 Departure for dinner

   7:30 Dinner at Ranch

   9:00-10:00 Keynote address: Scheraga, Overview of protein folding


tuesday, June 28

Folding and binding


   7:30 Continental breakfast

        Session chair: Marshall

   8:30 Scheraga, The protein folding problem: structure and folding pathways

   9:00 Brooks, Mechanism and energetics of insertion, folding and assembly of integral membrane peptides and proteins

   9:30 Jernigan, Representing protein dynamics with elastic networks

  10:00 Coffee break

  10:30 Levy, Effective potentials for protein folding and binding with applications using replica exchange simulations

  11:00 Kuczera, Modeling interactions of proteins involved in calcium signaling

  11:30 Wriggers, Probing the functional dynamics of protein assemblies by hybrid computational strategies

  12:00 Concluding remarks – Vakser, Vajda