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

Workshop Program:

Morning Session:

8:15-9:05       Breakfast and Registration

9:05-9:10  	Welcome and Greeting:
                Fred Roberts, DIMACS Director

9:10-9:20       Workshop Introduction 
                Casimir Kulikowski, Department of Computer Science, 
		Rutgers University

9:20-9:40       Structure Based Functional Genomics
                Gaetano T. Montelione, Department of Molecular Biology and
		Biochemistry, Rutgers University

9:40-10:30      The classification of Immunoglobulin-like proteins
                A. Kister and I. Gelfand, Department of Mathematics, 
		Rutgers University.

10:30-10:50     Break   

10:50-11:30     The Fold Rush - A Useful Lesson from Protein Classification
                Michal Linial, Department of Biological Chemistry, 
                The Hebrew University of Jerusalem, Israel
		
11:30-12:10     Accuracy of pair-wise protein sequence alignment:
                From observations to a new approach
                M.A. Roytberg, Institute of Mathematical Problems in Biology, 
                Pushchino, Russia
		
12:10-1:20 PM   Lunch

Afternoon Session:
        
1:20-1:50       Alignment scores as kernel functions in a regularized
                support vector classification method for fold recognition
                of remote protein families
                Vadim Mottl', Deparment of Cybernetics, Tula University, 
                Tula, Russia 

1:50-2:30       Parsing of structural protein domains from sequence data
                Casimir Kulikowski, Department of Computer Science, 
		Rutgers University

2:30-3:00       Building the Protein Family Invariant: correlation matrix
                Boris Galitsky and Sergey Shelepin, AskWeb, Inc.,
                Waltham, Massachusetts

3:00-3:40       Combinatorial model for revealing shelled cores in
                biomolecular structures
                B. Mirkin, School of Computer Science and Information Systems,
                Birkbeck College, London
              
3:40-4:00       Break

4:00-4:40       Analysis of Genomes and Transcriptomes in terms of the Occurrence of
                Protein Parts and Features
                Mark Gerstein, Molecular Biophysics and Biochemistry and 
                Computer Science, Yale University

4:40-5:20       Multiple Sequence Alignment Based on the Quasi-concave function
                Optimization Over a Lower Semi Lattics
                L. Shvartser, NESS A.T.Ltd-TSG, Tel-Aviv, Israel
 
5:20-6:30       Reception and Roundtable Discussion

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