This extension lets you align multiple sequences and structures of proteins.

Documentation

• Launch the Protein Aligner with the Home > Align command.
• Click either 'Align sequences (by structure)' or 'Align sequences (by chain)' to compute the alignment. Hovering on a sequence highlights the corresponding structure in the viewport.
• Click one of the 'Align to this' button to align the other structures on the corresponding structure.
• Click 'Highlight residues' to color residue letters according to their biophysical properties (hydrophobic, polar, etc.).

You can save the alignment to the clipboard or to the disk, in the FASTA format.

Important: structural alignment is performed based on the currently selected residues. Select a subset of residues to align structures based on these residues only (fe.g., where chains or structures have high local similarity).

Full tutorial: Aligning proteins.

References

This extension is based on the MUSCLE tool and was originally created by Guillaume Pages as part of his research work at NANO-D, Inria.