- Structure databases
- Comparative analysis
- Structure prediction
- Structural genomics
- Protein-protein & protein-ligand interactions
- Sequence-structure-function relationships
- Protein dynamics
- Data modeling, ontologies and query languages
- High performance computing as applied to genomics and proteomics
- Multimedia publishing
- Database-literature integration
Biological Systems Studied:
- Cell signaling
- B and T cell receptors
Specific Target Areas
- Off-target and repositioning of major pharmaceuticals
- Improving access and usability of biological data, standards and methods associated with macromolecular structure.
- Mapping protein fold space, automated classification of proteins according to sequence structure and function.
- High throughput proteomics to provide putative structural and functional annotation for use in comparative proteomics.
- Standards development develop new ontologies, expand existing ontologies, provide benchmark data.
- Protein structure prediction aided by deuterium exchange mass spectrometry.
- Epitope prediction.
- Evolution studied through protein fold, domain, family and superfamily distributions.
- Sequence-structure-function relationships in protein kinases.
- Functionally flexible regions in protein families.
- Prediction of sites of protein interaction and the complexes themselves.
- Development of reusable visualization tools.
- Multimedia-based dissemination of science.
- The RCSB Protein Data Bank (PDB) is in many ways the production arm of our research efforts.
- The Immune Epitope Database (IEDB)
- Mapping protein fold space - Comparing the 3D structures of proteins is non-trivial. We have developed algorithms for pairwise and multiple structure alignment.
- Protein domain assignment and classification, in 3-D,
- SciVee (SciVee)– integration of video and sound content with original publications.
- BioLit (biolit) - integration of literature and database content.
- Representing data on protein families -. The Apoptosis Database characterizes domains known to be involved in apoptosis.
- 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.