Research Interests

Last Update July 2007

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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...

• Improving access and usability of biological data 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.
• Prediction of ligand binding and off-target binding of pharmaceuticals
• Development of reusable visualization tools.
• Multimedia-based dissemination of science

Pointers...

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. SciVee (SciVee)– integration of video and sound content with original publications.
5. Representing data on protein families - The Protein Kinase Resource characterizes sequences and structure of the protein kinase family. The Apoptosis Database characterizes domains known to be involved in apoptosis.
6. 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.