Physical geometric algorithms for structural molecular biology

This paper surveys our recent work in three key areas, using a physical geometric algorithm approach to data interpretation, experiment planning, and drug design: 1) data-directed computational protocols for high-throughput protein structure determination; 2) an experiment planning and data interpretation algorithms for reducing mass degeneracy in mass spectrometry; and 3) computer-aided drug design tools and applying them to the design of an inhibitor for the core-binding factor-β on-coprotein (CBFβ-MYII11), a fusion protein involved in some forms of acute myclomonocytic leukemia. Our long-range goal is the structural and functional understanding of biopolymer interactions in systems of significant biochemical as well as pharmacological interest. The research overviewed here represents a set of important steps towards that goal.