Proteomes and Proteins

A Course Jointly Organized by
The International School of Advanced BioMedicine and BioInformatics
and by
The Lipari International  School for Computer Science Researchers

Lipari Island, July 9-22, 2006

The proteome is the specific protein complement of each cell. Proteomics, the analysis of proteomes’ structure and functional organization including protein post-translation modifications and protein-protein interactions (Interactomics), represents one of the frontiers of contemporary biomolecular and biocomputational research. In conjunction with Genomics, it will allow to understand how genotypes become phenotypes (eg, the relationship between the nucleotide sequence of a gene and the tridimensional structure of its encoded protein) as well as the dynamic interactions between organisms and the environment, including pathological modifications of their molecular phenotype. Besides making possible the identification of new targets for disease diagnosis and treatment, Proteomics will also allow to predict ligand-receptor binding,  a critical step both for a thorough understanding of the specificity of molecular interactions and for the discovery of new drugs. Finally, Proteomics will uncover potential toxic side effects during drug screening thus guiding the optimization process. In light of this, in 2006 the International School of Advanced BioMedicine and BioInformatics and the Lipari International School for Computer Science Researchers are jointly organizing a course on Proteomes and Proteins, aimed at describing the state of the art knowledge on proteomes, their dynamic changes during the life cycle of cells and organisms, their modifications in disease states as well as the applications of this knowledge to Molecular Medicine, Biotechnology and Medicinal Chemistry.



First Week (July 9-15)

  • Peter Greenberg, Washington University, USA
    - Sociomicrobiology: Proteins involved in bacterial quorum sensing and biofilm formation

  • Sorin Istrail, Brown University, USA
    - Protein-DNA interactions: Logic functions of the genomic cis-regulatory code
    - Protein structure alignment: rigorous algorithms
    - Mathematically and physically rigorous algorithms for protein lattice models

  • Michael Levitt, Stanford University, USA
    - Fundamental Interactions in Structural Biology
    - Understanding protein structure
    - Simulating atomic motion

  • Lance Liotta, George Mason University, USA
    - Oncoproteomics

  • Bud Mishra, New York University, USA
    Computational Oncogenomics
    - Cancer and Genomics: What we know and what we do not
    - Cancer and Computational Genomics: What we can compute and what we cannot
    - Cancer and Systems Biology: What we can predict and what we cannot

  • Gene Myers, Howard Hughes Medical Institute-Janelia Farms, USA
    - Imaging for understanding the meso-scale of the cell

  • Serge Przedborski, Columbia University, USA
    - Neurodegeneration: What it is and Where we are
    - Parkinson's Disease: Mechanisms and Models


Second Week (July 15-22)

  • Leslie Kuhn, Michigan State University, USA
    - Introduction to Structure-Based Docking and Virtual Screening
    - Representing the Shape, Chemistry, and Flexibility of Proteins and Ligands in Docking
    - Considerations in Achieving Ligands that are Specific to a Protein Target and Don't Bind to Homologous Proteins

  • Valerio Pascucci, Lawrence Livermoore, USA
    - Advanced Techniques for Data Analysis and Visualization.
    - Principles of integrated analysis and visualization for real-time data exploration.
    - Scalable visualization techniques for interactive navigation in high resolution data.
    - Topological analysis for feature extraction and guided data exploration.

  • Kimberly A. Watson, University of Reading, UK
    - Protein Structure and Function
    - An overview of Structural Genomics
    - Structural Genomics and Designer Drugs - Fact or Fiction?
    - Protein Interactions - Implications for Structure Based Drug Design



Directors of the School

Directors of the Course

A. Ferro
(University of Catania)

M. Purrello
(University of Catania)

A. Ferro
(University of Catania)
C. Guerra
(University of Padova, Italy - Georgia Tech, USA)
M. Purrello
(University of Catania)

Scientific Committee
R. Bernardini, N. Crimi, R. De Maria, V. De Pinto, C. Di Pietro, A. Ferro, E. Garaci, D. Garozzo, R. Giugno,
S. Guccione, C. Guerra,
A. Messina, A. Modesti, A. Pulvirenti,  M. Purrello, E. Rizzarelli, S. Stefani, M. Zappia

D. Barbagallo, P. Buffa, L. Giurato,
A. Laganą, M. Ragusa, M. Santagati