Commit
•
5c28821
1
Parent(s):
df569f4
Update README.md
Browse files
README.md
CHANGED
@@ -30,7 +30,8 @@ This model is trained to predict general binding sites of proteins using on the
|
|
30 |
`esm2_t6_8M_UR50D`, trained on [this dataset](https://huggingface.co/datasets/AmelieSchreiber/general_binding_sites). The data is
|
31 |
not filtered by family, and thus the model may be overfit to some degree. In the Hugging Face Inference API widget to the right
|
32 |
there are three protein sequence examples. The first is a DNA binding protein ([see UniProt entry here](https://www.uniprot.org/uniprotkb/D3ZG52/entry)).
|
33 |
-
Note there is nontrivial (GMPGTGK) overlap in the predicted binding sites and the binding sites given in UniProt.
|
|
|
34 |
|
35 |
The second and third were obtained using [EvoProtGrad](https://github.com/Amelie-Schreiber/sampling_protein_language_models/blob/main/EvoProtGrad_copy.ipynb)
|
36 |
a Markov Chain Monte Carlo method of (in silico) directed evolution of proteins based on a form of Gibbs sampling. The mutatant-type
|
|
|
30 |
`esm2_t6_8M_UR50D`, trained on [this dataset](https://huggingface.co/datasets/AmelieSchreiber/general_binding_sites). The data is
|
31 |
not filtered by family, and thus the model may be overfit to some degree. In the Hugging Face Inference API widget to the right
|
32 |
there are three protein sequence examples. The first is a DNA binding protein ([see UniProt entry here](https://www.uniprot.org/uniprotkb/D3ZG52/entry)).
|
33 |
+
Note there is nontrivial (GMPGTGK) overlap in the predicted binding sites and the binding sites given in UniProt. Note also that
|
34 |
+
some of the extraneous predictions are near misses and are very close to the binding sites given in UniProt.
|
35 |
|
36 |
The second and third were obtained using [EvoProtGrad](https://github.com/Amelie-Schreiber/sampling_protein_language_models/blob/main/EvoProtGrad_copy.ipynb)
|
37 |
a Markov Chain Monte Carlo method of (in silico) directed evolution of proteins based on a form of Gibbs sampling. The mutatant-type
|