Shula Shazman

Shula Shazman

Titles

Lecturer, The Open University of Israel

Phone

(212) 851-4656

I am currently concluding my postdoctoral studies in the Honig Lab. Recently, in collaboration with Richard Mann, we introduced a new database called OnTheFly for Drosophila melanogaster transcription factors and their binding sites. Briefly, this database integrates, in one location, structural and sequential information for both protein and DNA. Such a combined database is unique and can substantially contribute to our understanding of protein-DNA recognition processes, thereby leading to novel mechanistic conclusions and suggesting new candidates for experimental procedures and drug designs.

I am trained in both computer science (BSc) and biological sciences (MSc and PhD). My PhD thesis, under the supervision of Yael Mandel-Gutfreund at the Technion Israel, focused on computational approaches for the study of protein-RNA interactions. I developed a method for extracting and displaying positive electrostatic patches on the protein surface. This method, termed PFplus, is applicable for identifying functional interfaces on proteins, especially nucleic acid binding interfaces. By applying PFplus and using a machine-learning approach we predicted nucleic acid-binding functions based on the electrostatic properties of proteins. This prediction method was published in PLoS Computational Biology and was later validated experimentally in collaboration with Haim Manor at the Technion.


Education History

PhD, Technion, Israel Institute of Technology


Publications

Shazman S, Lee H, Socol Y, Mann RS, Honig B. OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. Nucleic Acids Res. 2014 Jan;42(Database issue):D167-71.

Dror I, Shazman S, Mukherjee S, Zhang Y, Glaser F, Mandel-Gutfreund Y. Predicting nucleic acid binding interfaces from structural models of proteins. Proteins. 2012 Feb;80(2):482-489.

Shazman S, Elber G, Mandel-Gutfreund Y. From face to interface recognition: a differential geometry approach to distinguish DNA from RNA binding surfaces. Nucleic Acids Res. 2011 Sep 1;39(17):7390-9.

Shazman S, Mandel-Gutfreund Y. Classifying RNA-binding proteins based on electrostatic properties. PLoS Comput Biol. 2008 Aug 8;4(8):e1000146.

Shazman S, Celniker G, Haber O, Glaser F, Mandel-Gutfreund Y. Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W526-30.


Address


Lab Staff