PDBEurope
/

Bioformer8L-ProteinStructure-NER-v0.1_onnx

 ---
 license: mit
+language:
+- en
+tags:
+- biology
+- protein structure
+- token classification
+widget:
+- text: "N-terminal acetylation (Nt-acetylation), carried out by N-terminal acetyltransferases (NATs), is a conserved and primary modification of nascent peptide chains. Naa60 (also named NatF) is a recently identified NAT found only in multicellular eukaryotes. This protein was shown to locate on the Golgi apparatus and mainly catalyze the Nt-acetylation of transmembrane proteins, and it also harbors lysine Nε-acetyltransferase (KAT) activity to catalyze the acetylation of lysine ε-amine. Here, we report the crystal structures of human Naa60 (hNaa60) in complex with Acetyl-Coenzyme A (Ac-CoA) or Coenzyme A (CoA). The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the β7-β8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures. Remarkably, we found that the side-chain of Phe 34 can influence the position of the coenzyme, indicating a new regulatory mechanism involving enzyme, co-factor and substrates interactions. Moreover, structural comparison and biochemical studies indicated that Tyr 97 and His 138 are key residues for catalytic reaction and that a non-conserved β3-β4 long loop participates in the regulation of hNaa60 activity."
+model-index:
+- name: Bioformer8L-ProteinStructure-NER-v0.1_onnx
+  results:
+  - task:
+      name: NER
+      type: token-classification
+    metrics:
+    - name: NER Precision
+      type: precision
+      value: 0.88
+    - name: NER Recall
+      type: recall
+      value: 0.92
+    - name: NER F Score
+      type: f_score
+      value: 0.90
 ---
+| Feature | Description |
+| --- | --- |
+| **Name** | `Bioformer8L-ProteinStructure-NER-v0.1_onnx` |
+| **Default Pipeline** | `transformer`, `ner` |
+| **Components** | `transformer`, `ner` |
+| **Vectors** | 0 keys, 0 unique vectors (0 dimensions) |
+| **Sources** | n/a |
+| **License** | n/a |
+| **Author** | [Melanie Vollmar]() |
+### Label Scheme
+<details>
+<summary>View label scheme (20 labels for 1 components)</summary>
+| Component | Labels |
+| --- | --- |
+| **`ner`** | "bond_interaction", "chemical", "complex_assembly", "evidence", "experimental_method", "gene", "mutant", "oligomeric_state", "protein", "protein_state", "protein_type", "ptm", "residue_name", "residue_name_number", "residue_number", "residue_range", "site", "species", "structure_element", "taxonomy_domain" |
+</details>
+### Scores for entity types
+| entity type | precision | recall | F1 | sample number|
+| --- | --- | --- | --- | --- |
+| "bond_interaction" | 0.95 | 0.88 | 0.91 | 39 |
+| "chemical" | 0.84 | 0.91 | 0.88 | 598 |
+| "complex_assembly" | 0.82 | 0.87 | 0.84 | 189 |
+| "evidence" | 0.79 | 0.90 | 0.84 | 420 |
+| "experimental_method" | 0.82 | 0.82 | 0.82 | 313 |
+| "gene" | 0.71 | 0.84 | 0.77 | 26 |
+| "mutant" | 0.85 | 0.90 | 0.87 | 219 |
+| "oligomeric_state" | 0.92 | 0.96 | 0.94 | 116 |
+| "protein" | 0.91 | 0.95 | 0.93 | 755 |
+| "protein_state" | 0.76 | 0.86 | 0.81 | 578 |
+| "protein_type" | 0.81 | 0.86 | 0.81 | 295 |
+| "ptm" | 0.70 | 0.72 | 0.71 | 33 |
+| "residue_name" | 0.87 | 0.90| 0.88 | 74 |
+| "residue_name_number" | 0.94 | 0.98 | 0.96 | 270 |
+| "residue_number" | 0.52 | 0.92 | 0.66 | 55 |
+| "residue_range" | 0.68 | 0.77 | 0.72 | 40 |
+| "site" | 0.86 | 0.90 | 0.88 | 250 |
+| "species" | 0.97 | 0.97 | 0.97 | 74 |
+| "structure_element" | 0.89 | 0.92 | 0.91 | 756 |
+| "taxonomy_domain" | 0.99 | 0.93 | 0.96 | 78 |