Molecular Modeling and Bioinformatics

SymD (Symmetry Detection)

Introduction

SymD is a tool for detecting internally symmetric protein structures. It works through an “alignment scan” procedure in which a protein structure is aligned to itself after circularly permuting the second copy by all possible number of residues. For each circular shift, one optimal, non-self structural alignment is kept, fully allowing gaps and unaligned loops. It uses the SE and RSE algorithms for finding the optimal structural superposition and refining the structure-based sequence alignment starting from each given circularly permuted initial alignment.

SymD reports T-score, which is a weighted number of aligned residues (sum(1/(1+(dij/do)^2))), and the Z-score of the T-score of the refined alignment at each position of the alignment scan and declares the structure symmetric if the maximum Z-score is greater than a given cutoff value. SymD also outputs the transformed structure at the position of the best Z-score, as well as the symmetry axis, the rotation angle and any translation along the symmetry axis (for helical symmetry). See the SymD Manual and Examples and refer to BMC Bioinformatics 2010 11:303.