SEA26

This is the documentation for the new version of SEA by Yujin Wu and Khanh Tang.

Software is open source

(link to github?)

how to do an alignment

• co-fold the query ligand and separately a similar ligand
• download both to your computer (takes 10 mins +)
• use chimeraX (UCSF ChimeraX) to load the CIF file of each
• use matchmaker #2 #1 to align the proteins
• use select ligand to focus on the ligand.
• visually inspect the query ligand and the most similar annotated ligand.
• do they occupy the same space?
• do they interact with the same residues?
• do the small molecules align in the part of the molecule that is recognized by the protein?
• evaluate whether it seems likely that this prediction is correct? that your query ligand would be expected to recapitulate the same interactions as a known ligand.
• check also for any available experimental structures in the PDB and consider aligning them.