I am using Bioinformatic tools to study proteins and DNA. During my PhD I integrated large scale structural information with conserved protein sequence motifs (from the Blocks database). The aim of this analysis is to learn which structural traits characterize conserved sequence regions.

My CV.

contact: einat.sitbon AT weizmann.ac.il

PUBLICATIONS

Sitbon E. and Pietrokovski S., Protein structure elements occurrence in conserved regions. Accepted to BMC Structural Biology.

Sitbon E. and Pietrokovski S., Secondary structure transitions and motifs in conserved sequence regions correlating sequence, structure and function. Submitted.

Sitbon E. and Pietrokovski S., New types of conserved sequence domains in DNA-binding regions of homing endonucleases, Trends Biochem Sci, 2003 Sep;28(9):473-7. [PubMed]

Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z and Godzik A., Using an alignment of fragment strings for comparing protein structures, Bioinformatics (ECCB 2006 supplemental), in press.

Amitai G., et. al., Network analysis of protein structures identifies functional residues, J Mol Biol, 2004 Dec 3;344(4):1135-46. [PubMed]

Kunin V., et. al., Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs, J Mol Biol, 2001 Mar 30;307(3):939-49 [PubMed]




My master thesis: Homing endonuclease like proteins - a computational and biochemical analysis .

Links:

Here you can find out if there are any NUMODs (nuclease-associated modular DNA-binding domains ) in your protein.

Is there a Destruction box in your protein? Dana Reichmann's site.

Where is the functional sites in a structure? check out SARIG.

Want to multiple align a multiple alignment to a multiple alignment database? Use LAMA
Or use CYRCA to check if it is consistently aligned.

Some more sequence alignment links.

LittleStone is a forum (both real and virtual) for discussing bioinformatic issues.