Global visualization of enzyme interaction space


Michael Farnum and Sergei Izrailev. 3-Dimensional Pharmaceuticals, Inc, 665 Stockton Dr, Exton, PA, PA 19341
Driven by the wealth of information provided by the genomics revolution, functional classification of large numbers of proteins has been performed on the basis of both sequence and structure comparisons. The appearance of databases containing protein-ligand interaction data for large numbers of protein classes and chemical compounds created the possibility of performing functional classification analyses with chemical genomics data. We demonstrate a technique for computing the relationships between enzymes and enzyme classes based on the properties of their small-molecule interaction partners. The method allows calculation of distances between each proteinís ligands using a variety of point set similarity measures. Combined with advanced dimensionality reduction techniques, this leads to novel visualizations of groups of enzymes based on their chemical affinities, which can aid in finding and interpreting complex functional relationships.

Chemogenomics: What It Is And What It Is Not
9:00 AM-11:30 AM, Wednesday, August 25, 2004 Pennsylvania Convention Center -- 201C, Oral

Biotechnology Secretariat

The 228th ACS National Meeting, in Philadelphia, PA, August 22-26, 2004