Dobbs Lab

Our long-term research goals are to understand how proteins and nucleic acids achieve their functional three-dimensional structures and to elucidate rules that dictate interactions between proteins, nucleic acids and other molecules in cells.  In collaboration with several groups on campus, we have begun to integrate computational and experimental approaches to explore sequence-structure-function relationships in macromolecular complexes.  Current areas of focus include: prediction  and validation of ligand binding residues in proteins (for  protein, DNA, RNA and small molecules), rational design of zinc finger DNA binding proteins, and prediction of functional effects of SNPs in unannotated proteins.

Selected Publications:

• Cao H., Ihm Y., Wang, C.Z., Morris, J.R., Su, M., Dobbs, D. and Ho, K.M. (2004) Three-dimensional threading approach to protein structure recognition, Polymer 45:687-697.
• Lonosky, P.M., Zhang, X., Honavar, V., Dobbs, D.L., Fu A., and Rodermel, S.R. (2004) A proteomic analysis of chloroplast biogenesis in maize. Plant Physiol. 134:560-574.
• Yan, C., Dobbs, D., and Honavar, V. (2004) A two-stage classifier for identification of protein-protein interface residues. Bioinformatics. 20:i371-i378.
• Sen, T.Z., Klockzkowski, A., Jernigan, R.L., Yan, C., Honavar, V., Ho, K., Wang, C, Ihm, Y., Cao, H., Gu, X., and Dobbs, D. (2004) Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics. 5:205.
• Terribilini, M., Lee, J.-H., Yan, C., Jernigan, R., Carpenter, S., Honavar, V., and Dobbs, D. (2006) Identifying interaction sites in "recalcitrant" proteins: Predicted protein and RNA binding sites in Rev proteins of HIV and EIAV agree with experimental data. Pac Symp Biocomput (PSB 2006) Singapore: World Scientific Press. pp. 415-426.
• Lee, J.-H., Murphy, S., Belshan, M., Sparks, W., Wannemuehler Y., Liu, S., Hope, T., Dobbs, D. and Carpenter, S. (2006) Characterization of functional domains of equine infectious anemia virus Rev suggests a bipartite RNA-binding domain, J  Virol. 80:3844-3852.
• Yan, C., Terribilini, M., Wu, F., Jernigan, R.L., Dobbs, D. and Honavar, V. (2006). Identifying amino acid residues involved in protein-DNA interactions from sequence. BMC Bioinformatics. In press.
• Terribilini, M. Lee, J.-H., Yan, C., Jernigan, R., Honavar, V., and Dobbs, D. (2006) Computational prediction of RNA-binding sites in proteins based on amino acid sequence, To appear