Olivia Viessmann

Shift of UMAP points when using .transform()

3

Hi, I am encountering a point shift issue when fitting umap to embeddings X_train and then applying the fit to embeddings X_test not seen during training. Here is an example...

Openfold not compatible with newest Flash attention 2.0.4

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Hi, I upgraded to flash attention 2.0.4, which breaks imports in the OpenFold package. Will there be an upgrade to make OpenFold compatible? Thanks Here the traceback: `Traceback (most recent...

Hi, I am using pymol to generate surface meshes from pdb source files. I would like to have the vertices in the same reference frame as the original pdb coordinates....

Hi, I have a question about the completeness of the complexes in DIPS-Plus. I find many complexes in DIPS-Plus that do not have a complete set of pairs for the...

Hello, first of all -- thank you for your work and contribution of Dips-plus to the community. I think this is a very valuable dataset and the documentation is awesome....

Training script for ff2

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Hi, great work on FF2 -- I would love to replicate it, but the trianing script provided is for the previous version. Would it be possible to provide the training...

Retraining OpenFold on Cath4.2

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Hi, i was wondering if anyone has ever retrained OpenFold on a small dataset, e.g. Cath (4.2) to see how well/bad it does at small scale. I am curious for...