SATURDAY, JUNE 16

 6:00pm - 8:00pm Registration and Reception

 7:30 Continental breakfast
 8:30 Welcome – Organizers

INTRODUCTION: STRUCTURAL GENOMICS

 9:00 Skolnick, Prediction of protein structure and function on a genomic scale

PROTEIN-PROTEIN DOCKING  1
(structure prediction and binding simulation)
Session chair: McCammon

 9:30 Janin, Common structural principles of protein-protein and protein-DNA recognition
10:00 Nussinov, Protein-ligand associations: Algorithms, hot spots and populations
10:30 Coffee break
11:00 Olson, Predicting protein-protein interactions with SurfDock and AutoDock
11:30 Sternberg, Protein-protein docking protocol
12:00 Lunch

PROTEIN-PROTEIN DOCKING  2
Session chair: Janin

 1:30 McCammon, Building supramolecular structures
 2:00 Schreiber, Protein-protein association, from basic understanding to rational design and molecular docking
 2:30 Shoichet, Docking protein ligands in multiple conformations with strict energy functions
 3:00 Coffee break
 3:30 Ten Eyck, Problems and possible solutions in protein docking calculations
 4:00 Weng, Docking unbound proteins using shape complementarity, desolvation and electrostatics
 4:30 Vakser, Docking of protein models

POSTER SESSION

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

ENERGETICS AND PROTEIN STRUCTURE-FUNCTION RELATIONSHIPS
(energy landscapes, stability of complexes, functional assignment of protein structures, binding site prediction)
Session chair: Scheraga

 7:30 Continental breakfast
 8:30 Scheraga, Protein-folding and protein-protein interactions
 9:00 Honig, Combining Biophysics and Bioinformatics to understand protein-protein interactions
 9:30 Camacho, A biophysical pathway to docking
10:00 Coffee break
10:30 Gatchell, Scoring functions for protein docking
11:00 Kellogg, Energetics of biomolecular interactions from the perspective of the lowly water molecule. Can we estimate delta G with simple empirical hydropathy models?
11:30 Elcock, Predicting functional residues without using sequence data
12:00 Lunch

PROTEIN - SMALL MOLECULE INTERACTIONS
(modulation of protein interactions by small molecules, protein mimetics)
Session chair: Olson

 1:30 Verkhivker, Hierarchy of simulation models in predicting peptide-protein interactions from the binding energy landscapes
 2:00 Cochran, Peptide and small-molecule inhibitors of protein-protein interactions
 2:30 Verlinde, Stochastic approximation with smoothing
 3:00 Vajda, Computational mapping of proteins for the binding sites of small ligands
 3:30 Coffee break

DISCUSSION

 4:00 Moult, Possibility of a protein docking challenge

INTERACTING AND NONINTERACTING PROTEINS
(identification of interactions and pathways)
Session chair: Wodak

 7:30 Continental breakfast
 8:30 Laskowski, Predicting protein reactivity from the sequence alone
 9:00 Wodak, Biological function from molecular activities and cellular processes
 9:30 Marcotte, Genome-wide protein networks
10:00 Coffee break
10:30 Schwikowski, Challenges in visualizing interaction networks
11:00 Hogue, Interactions come of age with the BIND database
11:30 Tovchigrechko, Database of protein-protein interactions: A 3D structure approach
12:00 Concluding remarks