SymD webserver: a platform for detecting internally symmetric protein structures

Abstract

Internal symmetry of a protein structure is the pseudo-symmetry that a single protein chain sometimes exhibits. This is in contrast to the symmetry with which monomers are arranged in many multimeric protein complexes. SymD is a program that detects proteins with internal symmetry. It proved to be useful for analyzing protein structure, function and modeling. This web-based interactive tool was developed by implementing the SymD algorithm. To the best of our knowledge, SymD webserver is the first tool of its kind with which users can easily study the symmetry of the protein they are interested in by uploading the structure or retrieving it from databases. It uses the Galaxy platform to take advantage of its extensibility and displays the symmetry properties, the symmetry axis and the sequence alignment of the structures before and after the symmetry transformation via an interactive graphical visualization environment in any modern web browser. An Example Run video displays the workflow to help users navigate. SymD webserver is publicly available at http://symd.nci.nih.gov.

Figure 1.

The SymD webserver alignment scan output. (A) Clicking the Eye icon displays the file in the Detail panel. (B) Clicking the ScatterPlot hyperlink displays the Z-score versus Initial Shift and the Z-score versus Angle interactive scatter plots. The six signal peaks in the example plot indicate that the domain has a 7-fold symmetry. Hovering the cursor over a point in the scatter plot displays the x- and y-coordinates of the point.

Figure 2.

The SymD webserver transformed structure output. (A) Clicking the Eye icon displays the PDB-format file in the Detail panel. (B) Clicking the Jmol hyperlink displays the original and transformed structures and the symmetry axis in Jmol. The coordinates of the structures and the axis can also be downloaded by clicking the Disc icon.

Figure 3.

The SymD webserver output of the sequence alignment. (A) Clicking the Eye icon displays the FASTA format file in the Detail panel. (B) Clicking the Jalview hyperlink displays the sequence alignment in Jalview. The FASTA format file can also be downloaded by clicking the Disc icon.