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OpenBioML / protein-lm-scaling

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Prepare ColabFoldDB #29

Open NZ99 opened 10 months ago

NZ99 commented 10 months ago

Download and prepare ColabFoldDB on the cluster.

ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. They are the backend of our ColabFold MMseqs2 searches.

https://colabfold.mmseqs.com/

jamaliki commented 10 months ago

/take

Geraldene commented 10 months ago

happy to take this on

NZ99 commented 10 months ago

cc @jamaliki @Geraldene let me know if any help is needed, I can start pulling it on the cluster in the meantime

Geraldene commented 10 months ago

thanks @NZ99 is cluster access available to everyone? sorry I might have missed a few messages

NZ99 commented 8 months ago

Sorry @Geraldene, had not seen this. Cluster access is restricted to significant contributors unfortunately. In any case ColabFoldDB is now available on our openbioml bucket, let me know if anyone wants to collaborate re: any processing that needs to be done, happy to help.

Geraldene commented 8 months ago

Happy to help with the processing @NZ99 :)