RosettaCommons
Instructions for generating MSA
Do you have instructions for how to generate the MSAs in some more details or can you refer to other documentation for how to generate it?
I'll leave it to others to provide more details about the exact parameters used with the paper, but you'll likely get decent results using MMseqs2-generated MSAs. (This is what most of the "third generation" AI structure prediction programs are now using, and was used for some of the paper.) This can be installed locally (https://mmseqs.com/), but as that requires installing a rather large database, most people use a webserver, either the official server at https://toolkit.tuebingen.mpg.de/tools/mmseqs2 or using the Colabfold API.
