Evaluate Alignment Reliability
The scores calculated by SQUARE can give you an important insight into the quality of your alignment. Regions defined as reliably aligned here are much more likely to have the correct structural alignment.
The Necessary Tools for Alignment Improvement
By using SQUARE in conjunction with the optimal alignments, secondary structure information, functionally important sites and conserved residues, you have the ability to improve your alignments.
Convert Alignments into Folds
The server will convert a sequence structure alignments into a CA trace, using the structure of the template. By sending the alignment you will automatically generate the model CA trace.
A Range of Alignment Formats
SQUARE is now able to accept alignments in a dozen formats, though we still prefer FASTA. You can check the list of formats accepted at this link.
Enter PDB code for template chain
(i.e. "1abc" or "1abcD") -->
Paste the two aligned sequences below. The template (PDB) sequence MUST be the second sequence. The preferred format is FASTA but other formats are now allowed.
Optimal alignment scores for comparison
Reconstruct folds from your alignments
Colour-coded PDB files also show alignment reliability scores
An explanation of the method
The process in graphical form
Score interpretation and annotated output examples
SQUARE. It's not as deep as a well nor as wide as a church door.