Customized Home Page: Structure Comparison Tool
The RCSB PDB homepage is comprised of web widgets that can be moved around, minimized, or hidden so users can create a website that reflects their interests. Frequently-used features can be moved to the top, while less popular items can be hidden or collapsed.
The Structure Comparison Tool widget can be added so that it appears every visit to the RCSB PDB home page. The tool calculates pairwise sequence (blast2seq, Needleman-Wunsch, and Smith-Waterman) and structure alignments (FATCAT, CE, Mammoth, TM-Align, TopMatch).
Comparisons can be made for any protein in the PDB archive and for customized or local files not in the PDB. Special features include support for both rigid-body and flexible alignments (via jFATCAT) and detection of circular permutations (via jCE).
To add this widget to the RCSB PDB home page, select the Customize This Page button from the left menu. Download Files, Sequence Search, and ADIT Deposition widgets can also be added or removed.
The Comparison Tool is also available as a web page and as a standalone Java Web Start application. Additional information is available online and as a flyer (PDF).