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(Shift to Fix secondary structure ElementS in Alignments)
A tool to refine pairwise protein sequence alignment, with a combination of sequence and structural scoring by locally shifting secondary structure elements.[Documentation]

Enter query and template sequences in either of these formats:
A pairwise alignment   or Two unaligned sequences

Or upload a file with sequences  

Upload a template (or template homolog) structure file in pdb format (Strongly recommended)
Template structure file:  
Or enter PDB identifier: Chain:

Email address to receive the result (Recommended)                 Job ID (optional)     


Choose a SFESA alignment refinement mode

Parameters Show/Hide



Tong J, Pei J, Otwinowski Z, Grishin NV. "Refinement by shifting secondary structure elements improves sequence alignments." Proteins. 2015 Mar;83(3):411-27. doi: 10.1002/prot.24746. Epub 2015 Jan 13.

Comments, suggestions and bug reports to:
Last modified: Wed June 24 15:10:07 CDT 2015