Skip to main content


Designing zinc finger DNA binding proteins

Research Achievements

Designing zinc finger DNA binding proteins

An interdisciplinary team of IGERT trainees and associates in the groups of V Honavar, (IGERT coPI, ISU, ComS), D Dobbs (IGERT PI, ISU, Genetics) and R Jernigan (IGERT advisor, Biophysics) reported the discovery of functional motifs and improved methods for prediction of B-cell and MHC epitopes in several 2008 & 2009 papers. The group also reported procedures for rigorous evaluation of software for identifying protein functional motifs, including epitope binding sites. These results exploited an interdisciplinary approach combining approaches from machine learning and theoretical biophysics. Publications include 1st author papers by IGERT students, including: Peto et al., in BMC Bioinformatics 9:487; Caragea et al. in BMC Bioinformatics 8:438 &10:S4; Lee et al., in Pac Symp Biocomput 13:501; as well as co-authored papers by Honavar and Dobbs, including El_Manzalawy, et al., in PLoS One 3:e3268, & J Mol Recognit. 21:243.