paired and unpaired MSA using local MMSEQ

[listofdina]

Is there a way to get MSA for multimers (homo/hetro) with the local MMSEQ similar to what the API outputs? I am running the version compiled from git, downloaded about a month and a half ago.

[martin-steinegger]

We currently do not support this but we have it on our todo list.

[martin-steinegger]

colabfold_search as well as colabfold_batch supports batch complex predictions. Just provide a fasta or csv fle with your complex sequences. Following is a example.fasta:

>1
PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK:PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK
>2 
PIAQIHILEGRSDEQKE:PIAQIHILEGRSDEQKETLIREVSEAISRSLDAPLTSVRVIITEMAKGHFGIGGELASK

You can search the databases, build the MSAs and predict the complex structures using the following commands:

colabfold_search example.fasta db msas
colabfold_batch msas predictions

Please update your local MMseqs2 to the newest version (see MMseqs2 repository).