This benchmark contains 2549 protein sequences used to test domain prediction performance by FUpred and RecCut on ESM-2 predicted contact maps.

To evaluate the predicted domains against the benchmark from FUpred and replicate the ESM-RecCut results in Table 2, you can run the following command:

```
python domain_evaluate.py --ref test.info --pred test.dom
```

To replicate the RecCut domain predictions, you can run the following command to generate the test.dom file:

```
python ../../src/make_db.py --fafile test.fasta --dbfile test
```

If you would like to replicate the FUpred predictions, you can first download the necessary contact map files with the following command:

```
wget -r -np -nd https://omics.informatics.indiana.edu/DCTprot/CE/
```

Then download the program from their link: https://zhanggroup.org/FUpred/download/FUpred.zip and simply call their binary file with any/all of the files located in the CE directory. Note that it will take much longer to run FUpred than RecCut for similar predictions.