DIMACS Working Group Meeting on Informatics of Protein Classification

December 15, 2000
DIMACS Center, Rutgers University, Piscataway, NJ

Organizers:
Casimir Kulikowski, Rutgers University, kulikows@cs.rutgers.edu
Guy Montelione, Rutgers University, guy@cabm.rutgers.edu
Ilya Muchnik, Rutgers University, muchnik@dimacs.rutgers.edu
Presented under the auspices of the Special Year on Computational Molecular Biology.

Co-sponsored by The New Jersey Commission on Science and Technology Initiative on Structural Genomics and Bioinformatics and by Rutgers Bioinformatics Initiative.

This workshop will investigate models of protein classification and protein interaction. It seems both impossible and unnecessary to describe in detail every unique protein. To understand how a protein's machinery works in a cell, one wants to develop an efficient classification of proteins. It is well accepted that such a classification should be based on particular pieces of proteins which are called domains. Unfortunately, there don't exist precise formal definitions of domains which are accepted by most experts, either for amino acid sequence or 3D-structure presentations of proteins. There are a few databases which present classifications and one can consider them to infer experimentally presented definitions. For instance, the SCOP database or FSSP are such databases for protein domains formed by structural data and PRODOM and PFAM are protein domain databases organized around sequence information. Acceptable formal definitions are important for genetic engineering, drug design, and other fields of modern biotechnology, because only through them can one build software to manipulate proteins in silico, and thus we will explore them in this workshop.

Comparison analysis is a fundamental part of many protein studies. We will pay particular attention to similarity measures for proteins in different representations. There are a lot of tools for such analysis, but we don't yet know the limits of their usefulness. Moreover, we know very litle about how existing tools can work together in some integrated way. We will discuss these questions in the workshop.

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Document last modified on November 7, 2000.