ColabDesign
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sokrypton
Making Protein Design accessible to all via Google Colab!
Dear authors, I found that the results of mk_af_model.predict and localcolabfold are quite different for prediction of 2-sequences complex. I wonder why there is such different? (I want to use...
First, thanks for creating this tool! Is it intentionally to input `target_id` and `binder_id` asymmetrically for `mask_1d` and `mask_ib` below? https://github.com/sokrypton/ColabDesign/blob/d193e44f77a8f382cdd8fdb49c565c17e61fa13a/colabdesign/af/loss.py#L42-L47 Inside `get_con_loss` there are are some logical_and operations, and...
Thank you very much for making such valuable tools publicly available. Could you clarify the license of `ColabDesign`? I noticed that `ColabDesign` is installed as a dependency for the recently...
I don't think the value was being passed to the MPNN model
Is there any plan on integrating ligandmpnn and membranempnn options in colabdesign? Thanks!
Could anyone provide me a stable virtual env? Or just the versions of each packages? I'm trying to install colabdesign locally, but facing multiple compatibility issues, with Jax or dm-haiku...
Hello there! I come to you since I am currently attempting to leverage AFdesign’s binder hallucination to redesign a sequence to bind a particular target. The thing is that I...
This is more FYI than actual issue. python 3.9.13 colabdesign 1.1.1 pip will install dm-haiku v0.0.14 With this combination, the colabfold import fails. **Downgrading to dm-haiku==0.0.13 fixes the issue** Error:...
As of JAX 0.6.0 (April 16, 2025) [several tree functions have been removed](https://github.com/jax-ml/jax/blob/main/CHANGELOG.md#jax-060-april-16-2025) >From jax: jax.treedef_is_leaf, jax.tree_flatten, jax.tree_map, jax.tree_leaves, jax.tree_structure, jax.tree_transpose, and jax.tree_unflatten. Replacements can be found in {mod}jax.tree or...
Hi there, I'm using a trimmed pdb to accelerate the binder design. However, occasionally I encountered the error: ValueError: cannot convert float NaN to integer. I'm not sure why NaN...
