Paul A. Clemons

Paul Clemons, director of computational chemical biology research for the Broad Institute’s Chemical Biology Program, leads a team of researchers that use small molecules – chemical compounds that may be precursors to drugs – to explore biology, especially disease biology. In collaboration with biologists, Clemons’s team helps interpret the consequences of interactions between small molecules and cells, especially those with characterized genetic makeup. Clemons and his team use quantitative measurements and computational and visualization techniques to evaluate results. Clemons also analyzes the diversity of small-molecule collections and works with chemists to identify the consequences of synthetic chemistry decisions on small-molecule performance, with the goal of developing optimal collections of small molecules for biological discovery. Current research activities in the Clemons group include quantifying chemical diversity of small-molecule collections, understanding the genetic basis for small-molecule sensitivity, and using multidimensional analysis of large datasets resulting from small-molecule profiling to understand the mechanisms of action of novel small molecules.

As a graduate student, Clemons was a lead investigator in a large team effort to develop a “one-bead, one-stock solution” approach to chemical genetics, a precursor to the chemistry technology platform still in use by the Broad Institute. After receiving his Ph.D. in molecular and cellular biology from Harvard University, Clemons moved to the Harvard Institute of Chemistry & Cell Biology (ICCB), where he led additional technology development projects and conducted basic research to bring computational approaches to chemical-genetics research. In the context of the National Cancer Institute’s Initiative for Chemical Genetics, first at ICCB and later at the Broad, Clemons’s group helped develop tools such as ChemBank, a public, small-molecule structure and data analysis environment that life scientists can use.

Select Publications

Swamidass, SJ, Calhoun, BT, Bittker, JA, Bodycombe, NE, Clemons, PA. Utility-aware screening with clique-oriented prioritization. J. Chem. Inf. Model. (2012) 52: 29-37. PMCID: [PubMed – in process]

Clemons, PA, et al. Quantifying structure and performance diversity for sets of small molecules comprising small-molecule screening collections. Proc. Natl. Acad. Sci. USA, 2011 Apr 26;108(17):6817-22. Epub 2011 Apr 11.

Dancík V, Seiler KP, Young DW, Schreiber SL, Clemons PA. Distinct biological network properties between the targets of natural products and disease genes. J Am Chem Soc. 2010 Jul 14;132(27):9259-61.

Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, Ferraiolo P, Tolliday NJ, Schreiber SL, Clemons PA. ChemBank: a small-molecule screening and cheminformatics resource database. Nucleic Acids Res. 2008 Jan;36(Database issue):D351-9. Epub 2007 Oct 18.

Last updated date: May 2012