Research Interests

Last Update January 2009

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Research Areas

In General...

  • Structural bioinformatics:
  • Structure databases
  • Comparative analysis   
  • Classification
  • Structure prediction
  • Structural genomics
  • Protein-protein & protein-ligand interactions
  • Sequence-structure-function relationships
  • Evolution
  • Protein dynamics
  • Immunology
  • Information technologies:
  • Data modeling, ontologies and query languages
  • High performance computing as applied to genomics and proteomics
  • Workflows
  • Visualization
  • Multimedia publishing
  • Database-literature integration
  • Biological systems studied:
  • Cell signaling
  • Apoptosis
  • B and T cell receptors

Specific Projects Areas...


  1. The RCSB Protein Data Bank (PDB) is in many ways the production arm of our research efforts.
  2. The Immune Epitope Database (IEDB)
  3. Mapping protein fold space - Comparing the 3D structures of proteins is non-trivial. We have developed algorithms for pairwise and multiple structure alignment.
  4. Protein domain assignment and classification, in 3-D,
  5. SciVee (SciVee) integration of video and sound content with original publications.
  6. BioLit (biolit) - integration of literature and database content.
  7. Representing data on protein families -. The Apoptosis Database characterizes domains known to be involved in apoptosis.
  8. The molecular biology toolkit (mbt) is a toolkit for the Web delivery of high quality visuals of biological data, most notably macromolecular structure and uses Java3D.