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aqlaboratory / openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
Apache License 2.0
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About the evaluation in CASP14 #44

Open YiningWang2 opened 2 years ago

YiningWang2 commented 2 years ago

Hello everyone. I am doing some evaluation jobs of the inference pipeline. I am wondering how to evaluate the result pdb file such like TM-score, for those proteins that CASP14 doesn't provide the remarking pdb file.

gahdritz commented 2 years ago

If you use one of the sets of "_ptm" model weights, the model will output a predicted TM score in addition to the predicted structure, if that's what you're asking.

starkhu commented 1 year ago

i used "finetuning_ptm_2.pt" as openfold_checkpoint_path, running the inference command, but i only got pdb file and alignments dir, TM score was not seen in the log also. could anyone can provide a fasta file and its ground truth. and Using this fasta file as input, we run the inference program then can get a TM score.