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lhatsk / AlphaLink

AlphaLink: Integrating crosslinking MS data into OpenFold
Apache License 2.0
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Issue with multimer #6

Closed samuelmurail closed 1 year ago

samuelmurail commented 1 year ago

Hello,

I have been trying using AlphaLink with distance constraints between different subunits. From what I understand from the code, it doesn't seem possible to add such constraints.

Am I right ?

Cheers, Samuel

lhatsk commented 1 year ago

Hi Samuel,

Yes, AlphaLink currently only works for single-chain proteins. Multimer is in the works.

avilella commented 1 year ago

I'd be interested in using it for Multimer predictions/tuning as well.

lhatsk commented 1 year ago

We just released AlphaLink2 which can predict protein complexes: https://biorxiv.org/cgi/content/short/2023.06.07.544059v1

https://github.com/Rappsilber-Laboratory/AlphaLink2

The installation procedure will be a little more complicated and is currently only tested with a local installation. AlphaLink2 uses Uni-Fold and some memory optimisations.