SymD server: a platform for detecting internally symmetric protein structures

Tuesday, October 25, 2011 — Poster Session II
Noon – 2:00 p.m.	Natcher Conference Center	NCI	STRUCTBIO-7

Authors

• CH Tai
• R Paul
• D K.C.
• J Shilling
• BK Lee

Abstract

Many protein chains are made of repeating units of similar structures arranged in a beautifully symmetric manner. The mechanism of such an arrangement, their biological function, and their evolutionary history are largely unknown. To answer these questions, we developed SymD program to detect internally symmetric protein structures. Here, we report on the development of the SymD Web server (http://symd.nci.nih.gov), a dynamic platform based on Galaxy to determine if a protein is symmetric and to visualize the structure interactively. The input can be a user’s own structure or those fetched from PDB, SCOP or CATH protein structure database. The protein is aligned to itself after circularly permuting the second copy by all possible number of residues. SymD finds the transformation that will make the original and the permuted structures maximally aligned. Users can view the superposition between the original structure and the permuted structures and the rotation axis in Jmol on-line interactively. Their sequence alignment is displayed in Jalview. SymD server also shows scatter plots of symmetry measures. Users can also download the results and SymD executables from the Web site for further analysis.

back to top