DIMACS Workshop on Protein Domains: Identification, Classification and Evolution

February 27-28, 2003
DIMACS Center, CoRE Building, Rutgers University

Organizers:

Stephen Bryant, National Institutes of Health, bryant@ncbi.nlm.nih.gov

Teresa Przytycka, National Institutes of Health, przytyck@ncbi.nlm.nih.gov

Preliminary Program:

Thursday, February 27, 2003

 8:00 -  8:50  Breakfast and Registration

 8:50 -  8:55  Welcome and Greeting:
               Fred S. Roberts, DIMACS Director

 8:55 -  9:00  Welcome and Greeting:
               Steven Bryant, National Institutes of Health
               Teresa Przytycka,  Johns Hopkins University

Session I: Characterization of Protein Domains

 9:00 -  9:45  From the Hierarchic Organization of Domains
                 to Hierarchic Folding in 20 years
               George Rose, Johns Hopkins University 

 9:45 - 10:30  The Evolution of Structure and Function in CATH 
                 Protein Superfamilies
               Christine Orengo, University College London

10:30 - 11:00  Break

11:00 - 11:45  The Language of Proteins
               Alex Bateman, Sanger Institute, UK 

11:45 - 12:30  Recursive Domains in Proteins
               Teresa Przytycka, Johns Hopkins University

12:30 -  2:00  Lunch

Session II: Sequence Based Comparative Methods for Domain Identifications

 2:00 -  2:45  Assessing the accuracy of database search methods, and improving
               the performance of PSI-BLAST
               Stephen Altschul, National Center for Biotechnology Information 

 2:45 -  3:30  Discovery of Sequence-Structure Patterns across Diverse Proteins
               Bonnie Berger, MIT 

 3:30 -  3:45  Break

Session III:  Structure Based Comparative Methods for Domain Identifications

 3:45 -  4:30  Recurrent domains and domain space
               Liisa Holm, EMBL, European Bioinformatics Institute 

 4:30 -  5:15  Structure-Based Alignments of Conserved Domains
               Steven Bryant, National Institutes of Health

 5:15 -  6:00  Identification of Structural Domains in Proteins
               Marc A. Marti-Renom, The Rockefeller University

 6:00 -  7:00  Reception and poster session


Friday, February 28, 2003

 8:00 - 9:00   Breakfast and Registration

Session IV: Evolutionary Classification

 9:00 -  9:45  The domain structure of proteins: prediction and organization
               Golan Yona, Cornell University 

 9:45 - 10:30  Birth and death of protein domains and the power law behavior
               Yuri Wolf, NIH

10:30 - 10:45  Break

10:45 - 11:30  A Conserved Domain Database
               Aron Marchler-Bauer, National Center for Biotechnology Information 

11:30 - 12:15  Changes in Protein Repertoires that Underlay Increases in
                 Biological Complexity: the Immunoglobulin Superfamily in
                 Drosophila melanogaster and Caenorhabditis elegans
               Cyrus Chothia, MRC Laboratory of Molecular Biology

12:15 -  1:00  Analysis of common structural and sequence features of beta
                 sandwich and beta barrel proteins
               Alexander Kister, Rutgers University

 1:00 -  2:15  Lunch

Session V: Domain Interactions

 2:15 -  3:00  Evolution of Multi-Domain Proteins
               Sarah Teichmann, MRC Laboratory of Molecular Biology

 3:00 -  3:45  Protein Domain Research and Visualization Tools for
                 the Biomolecular Interaction Network Database
               Christopher Hogue, Samuel Lunenfeld Research Institute of 
                  Mt. Sinai Hospital, Toronto, Ontario

 3:45 -  4:30  Protein Interactions: Binding and Folding
               Ruth Nussinov, National Cancer Institute



Poster presentations:

    1. SUPFAM - Database of potential protein superfamily relationships 
       derived by comparing sequence-based and structure-based families: 
       Implications for structural genomics and function annotation in genomes.
         Shashi Bhushan Pandit (1) 
         S. Balaji1, V.S. Gowri (1) 
         K.R. Abhinandan (1)
         R. Vaishnavi (2)
         N. Srinivasan (1)
           (1) Molecular Biophysics Unit, Indian Institute of Science
           (2) Biotechnology Centre, Indian Institute of Technology

    2. Evolution of Multi-domain Proteins by Gene Fusion and Fission
         Sarah K. Kummerfeld, Christine Vogel, Mary Pacold & Sarah A. Teichmann
           MRC Laboratory of Molecular Biology

    3. Functional Fingerprints of Folds: Evidence for Correlated 
       Structure-Function Evolution.
         Boris E. Shakhnovich (1)
         Nikolay V. Dokholyan (2)
         Charles DeLisi (1) 
         Eugene I. Shakhnovich (3)
           (1)  Bioinformatics Department, Boston University,
           (2)  Department of Biochemistry and Biophysics, 
                  University of North Caroline at Chapel Hill, School of Medicine,
           (3) Department of Chemistry and Chemical Biology, Harvard University.

    4. Expanding protein universe and its origin from the biological big bang
         Nikolay V. Dokholyan (1)
         Boris Shakhnovich (2)
         Eugene I. Shakhnovich (3)
           (1)  Department of Biochemistry and Biophysics,                   
                  University of North Caroline at Chapel Hill School of Medicine
           (2)  Bioinformatics Department, Boston University
           (3) Department of Chemistry and Chemical Biology, Harvard University

    5. Hydrophobicity of Protein Domains: Spatially Profiling their Distribution
         Ruhong Zhou, Ajay Royyuru, Prasanna Athma, and B. David Silverman             
           IBM Thomas J. Watson Research Center

    6. Possible 3D structural domain link in the interaction and roles of
       E2 and E3 related proteins
         Sarangan Ravichandran, Robert Stephens and Jack R. Collins
           Advanced Biomedical Computing Center, National Cancer Institute-SAIC

    7. Improving Profile Hidden Markov Models for Detection of Remote 
       Homologs through Introduction of Phylogenetic Inference
         Dawn Brooks and Sean Eddy
           Department of Genetics, Washington University

    8. Atomic Contact Vectors in Protein-protein Recognition
         Julian Mintseris & Zhiping Weng 
           Boston Univesity Bioinformatics

    9. Computational Mutagenesis Analysis of HIV-1 Protease: 
       A Statistical Geometry Approach
         Majid Masso and Iosif I. Vaisman
           Bioinformatics and Computational Biology, School of Computational
           Sciences, George Mason University 

   10. Consensus approach for benchmarking domain assignment in protein structures.
         Stella Veretnik (1)
         Nickolai Alexandrov (2)
         Phil Bourne (1)
         Ilya Shindyalov(1)
           (1) San Diego Supercomputer Center
           (2) Ceres, Inc.

   11. Using language modelling techniques from speech recognition to enhance
       protein domain detection
         Lachlan Coin
         Wellcome Trust Sanger Institute
   
   12. Protein Domains as Lexical Units of Cell Language
         Sungchul Ji
         Rutgers University

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