Update README.md

README.md

@@ -48,7 +48,7 @@ REXzyme is based on the [Efficient T5 Large Transformer](https://huggingface.co/
 and contains 48 (24 encoder/ 24 decoder) layers with a model dimensionality of 1024, totaling 770 million parameters. 
 
 REXzyme is a translation machine trained on portion the [RHEA database](https://www.rhea-db.org/) containing 20,911,485 reaction-enzyme pairs. 
-The pre-training was done on pairs of SMILES and amino acid sequences. Note that two seperate tokenizers were used for input (./tokenizer_smiles) and labels (./tokenizer_aa).
+The pre-training was done on pairs of SMILES and amino acid sequences. Note that two seperate tokenizers were used for input (./tokenizer_aa-ABPE_SMILES/tokenizer_ABPE_rexzyme_offset) and labels (./tokenizer_aa).
 
 REXzyme was pre-trained with a supervised translation objective  i.e., the model learned to process the continous
 representation of the reaction from the encoder to autoregressively (causual language modeling) produce the output. 
@@ -66,96 +66,7 @@ reaction classes.
 We converted the reactions from rxn format to smile string including only left-to-right reactions.
 The enzyme sequences were truncated to 1024.
 Enzymes catalyzing more than one reaction appear in multiple enzyme-reaction pairs.
-<br/><br/>
-- **General descriptors**
-
-    | Method                | Natural     | Generated <sup>[1]</sup> |
-    | :---                  |    :----:   |          ---:            |
-    | **IUPRED3 (ordered)** | 99.9%       | 99.9%                    |
-    | **ESMFold (avg. plddt)**            | 85.03       | 79.82  |
-    | **FlDPnn**            | 0.0878      | 0.0929                  |
-<sup>[1]|</sup> We excluded sequences with %identities ≥ 70% and pLDDTs < 60%.
-<br/><br/>
-
-
-- **Functional classification**
-<br/><br/>
-<table>
-  <tr>
-    <td><b>Method </b></td>
-    <td colspan="2"> <a href="https://google-research.github.io/proteinfer/">ProteInfer</a></td>
-    <td colspan="2"> <a href="https://www.science.org/doi/10.1126/science.adf2465">CLEAN</a></td>
-  </tr>
-  <tr>
-    <td><b>Dataset</b></td>
-    <td >Natural (%) </td>
-    <td >Generated (%) </td>
-    <td >Natural (%) </td>
-    <td >Generated (%) </td>
-  </tr>
-    <tr>
-    <td><b> EC: Level 1 </b></td>
-    <td >81</td>
-    <td >80</td>
-    <td >80</td>
-    <td >79</td>
-  </tr>
-    <tr>
-    <td><b> EC: Level 2 </b></td>
-    <td >78</td>
-    <td >77</td>
-    <td >79</td>
-    <td >78</td>
-  </tr>
-    <tr>
-    <td><b> EC: Level 3 </b></td>
-    <td >76</td>
-    <td >75</td>
-    <td >78</td>
-    <td >77</td>
-  </tr>
-    <tr>
-    <td><b> EC: Level 4 </b></td>
-    <td >62</td>
-    <td >58</td>
-    <td >70</td>
-    <td >65</td>
-  </tr>
-    <tr>
-    <td><b> No EC predicted </b></td>
-    <td >10</td>
-    <td >7</td>
-    <td >0</td>
-    <td >0</td>
-  </tr>
-    <tr>
-    <td><b> GO-Terms </b></td>
-    <td >41</td>
-    <td >39</td>
-    <td >-</td>
-    <td >-</td>
-  </tr>
-    <tr>
-    <td><b> No GO predicted </b></td>
-    <td >1</td>
-    <td >1</td>
-    <td >-</td>
-    <td >-</td>
-  </tr>
-</table>
-<br/><br/>
-- **PGP pipeline** [(see GitHub)](https://github.com/hefeda/PGP)
-
-    | Method      | Natural | Generated |
-    | :---        | :----   |      :--- |
-    | **Disorder**      | 11.473       | 11.467   |
-    | **DSSP3**   | L: 42%, H: 41%, E:18% | L: 45%, H: 39%, E: 16%|
-    | **DSSP8**   | C:25%, H:38% T:10%, S:5%, I:0%, E:19%, G:2%, B:0% | C:29%, H:38% T:10%, S:4%, I:0%, E:17%, G:3%, B:0%|
-    | **CATH Classes**   | Mainly Beta: 6%, Alpha Beta: 78%, Mainly Alpha: 16%, Special: 0%, Few Secondary Structures: 0% |  Mainly Beta: 4%, Alpha Beta: 87%, Mainly Alpha: 9%, Special: 0%, Few Secondary Structures: 0%|
-    | **Transmembrane Prediction**  | Membrane: 9%, Soluble: 91% | Membrane: 9%, Soluble: 91%|
-    | **Conservation**      | High: 37%, Low: 33%      | High: 38%, Low: 33%  |
-    | **Localization**   | Cytop.: 66%, Nucleus: 4%, Extracellular: 6%, PM: 4%, ER: 11%, Lysosome/Vacuole: 1%, Mito.: 6%, Plastid: 1%, Golgi: 1%, Perox.: 1% | Cytop.: 85%, Nucleus: 2%, Extracellular: 6%, PM: 1%, ER: 6%, Lysosome/Vacuole: 0%, Mito.: 4%, Plastid: 0%, Golgi: 0%, Perox.: 0%|
-<br/><br/>
+
 
 
 ## **How to generate from REXzyme**