My students and I work on interdisciplinary projects ... computer science, biology, and chemistry. Long-term projects include predicting structural properties of disease causing protein mutants, inferring the effects of indels, and stints into machine learning, PDZ domains, as well as big data. For many of these, we make source code and/or servers publicly available, such as at motifAnalyzerPDZ, Domain Analysis and Motif Matcher (DAMM), and Coarse-Grained Rigidity Analysis of Proteins (CRRAP).
In past work, my students and I developed a web server for an exhaustive screen enabling exploring the effects of amino acid substitutions via rigidity mutation maps, as well as drug resistance in silico screening methods.
Previously, I co-developed KINARI, with Naomi Fox and Ileana Streinu, a suite of graph-based algorithms for studying the flexibility of biomolecules. I designed, developed, and deployed KINARI-Mutagen, the first rigidity-based approach for inferring the effects of mutations.
Word Clouds for my most recent (pacman) and last 10 (rook) publications are shown right. My 800m PR is 1:50.17 (FAT).