Hi!
I want to generate a list of putative binding partners for my protein of interest by essentially BLASTing for the ligand which binds to EVH1 domains, FPxΦP. Is there a database where I could enter this, and it would search for all of the possible combinations of my motif? It seems that there are a ton of options out there, so I'm a little overwhelmed with trying to figure out which direction to go! Thanks in advance!
Sara
Hi Sara,
So you want to find a set of putative ligands and you already know at least one ligand, right? You can use blast to search for motifs with similar sequences, as you said. Additionally you can use CATH (http://www.cathdb.info) or SCOP (http://scop.berkeley.edu) to search for motifs with similar structure. Also string (https://string-db.org/cgi/input.pl) may help you finding putative ligands of the protein you are interested in. Good luck!
ML
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