Donald Petrey


Senior Computational Scientist

The development of computational approaches for the analysis of the relationship between protein structure and function. My work has involved the development of algorithms and software in different areas of the general problem, primarily the construction and evaluation of homology models, biophysical analysis of visualization of protein structures, and tools for structure comparison and the inference of function from structural similarity. These tools have been integrated into web-servers for model building, function annotation, and protein interface/interaction prediction.

Education History

PhD, Columbia University
Biochemistry and Molecular Biology

BSc, University of Maryland at College Park


Garzón JI, Deng L, Murray D, Shapira S, Petrey D, Honig B. A computational interactome and functional annotation for the human proteome. Elife (2016) 5:e18715.

Hwang H, Petrey D, Honig B. A hybrid method for protein-protein interface prediction. Protein Sci. (2016) 25:159-65.

Chen T.S., Petrey D., Garzon J., Honig B. (2015) Predicting peptide-mediated interactions on a genome-wide scale. PLoS Comp. Biol., in press.

Petrey D., Chen T.S., Deng L., Garzon J.I., Hwang H., Lasso G., Lee H., Silkov A., and Honig, B. (2015) Template-based prediction of protein function. Curr. Opin. Struc. Biol. 32, 33-38.

Petrey D., and Honig B. (2014) Structural Bioinformatics of the Interactome. Ann. Rev. Bioph. 43, 193-210.

Dey F., Zhang Q.C., Petrey D., Honig B. (2013) Toward a “Structural BLAST”: Using structural relationships to infer function. Protein Science 22, 359-366.

Zhang Q.C., Petrey D., Garzón J.I., Deng L., Honig B. (2013) PrePPI a structure-informed database of protein–protein interactions. Nucl. Acids Res. 41, D828-D833.

Zhang Q.C., Petrey D., Deng L., Qiang L., Shi Y., Thu C.A., Bisikirska B., Lefebvre C., Accili D., Hunter T., Maniatis, T., Califano, A., and Honig, B. (2012) Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490, 556-560.

Zhang Q.C., Deng L., Fisher M., Guan J., Honig B., Petrey D. (2011) PredUs: a web server for predicting protein interfaces using structural neighbors. Nucl. Acids Res. 39, W283-W287.

Kuziemko A., Honig B., Petrey D. (2011) Using structure to explore the sequence alignment space of remote homologs. PLoS Comp. Biol. 7, e1002175-e1002175.

Fischer M., Zhang Q.C., Dey F., Chen B.Y., Honig B., Petrey D. (2011) MarkUs: a server to navigate sequence–structure–function space. Nucl. Acids Res. 39, W357-W361.

Zhang, Q. C., Petrey, D., Norel, R., and Honig, B. H. (2010) Protein interface conservation across structure space. Proc. Natl. Acad. Sci. 107, 10896-10901.

Norel, R., Petrey, D., and Honig, B. (2010) PUDGE: a flexible, interactive server for protein structure prediction. Nucl. Acids Res. 38, W550-W554.

Lee, H., Li, Z., Silkov, A., Fischer, M., Petrey, D., Honig, B., and Murray, D. (2010) High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. J. Struct. Funct. Gen. 11, 51-59.