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  license: mit
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  license: mit
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+ language:
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+ - en
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+ tags:
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+ - biology
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+ - protein structure
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+ - token classification
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+ widget:
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+ - 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."
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+ model-index:
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+ - name: BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.4
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+ results:
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+ - task:
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+ name: NER
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+ type: token-classification
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+ metrics:
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+ - name: NER Precision
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+ type: precision
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+ value: 0.90
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+ - name: NER Recall
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+ type: recall
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+ value: 0.92
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+ - name: NER F Score
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+ type: f_score
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+ value: 0.91
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  ---
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+
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+
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+ | Feature | Description |
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+ | --- | --- |
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+ | **Name** | `BiomedNLP-PubMedBERT-ProteinStructure-NER-v1.4` |
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+ | **Default Pipeline** | `transformer`, `ner` |
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+ | **Components** | `transformer`, `ner` |
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+ | **Vectors** | 0 keys, 0 unique vectors (0 dimensions) |
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+ | **Sources** | n/a |
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+ | **License** | n/a |
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+ | **Author** | [Melanie Vollmar]() |
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+
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+ ### Label Scheme
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+
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+ <details>
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+
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+ <summary>View label scheme (19 labels for 1 components)</summary>
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+
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+ | Component | Labels |
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+ | --- | --- |
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+ | **`ner`** | "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" |
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+
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+ </details>
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+
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+ ### Scores for entity types
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+ | entity type | precision | recall | F1 | sample number|
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+ | --- | --- | --- | --- | --- |
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+ | "chemical" | 0.90 | 0.93 | 0.92 | 390 |
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+ | "complex_assembly" | 0.88 | 0.91 | 0.89 | 162 |
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+ | "evidence" | 0.86 | 0.89 | 0.88 | 272 |
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+ | "experimental_method" | 0.73 | 0.76 | 0.75 | 240 |
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+ | "gene" | 0.89 | 0.86 | 0.88 | 66 |
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+ | "mutant" | 0.93 | 0.95 | 0.94 | 495 |
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+ | "oligomeric_state" | 0.88 | 1.00 | 0.93 | 64 |
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+ | "protein" | 0.97 | 0.97 | 0.97 | 1017 |
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+ | "protein_state" | 0.78 | 0.85 | 0.81 | 363 |
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+ | "protein_type" | 0.84 | 0.90 | 0.87 | 262 |
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+ | "ptm" | 0.64 | 0.81 | 0.71 | 37 |
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+ | "residue_name" | 0.97 | 0.92 | 0.94 | 84 |
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+ | "residue_name_number" | 0.98 | 0.99 | 0.99 | 487 |
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+ | "residue_number" | 1.00 | 0.93 | 0.96 | 14 |
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+ | "residue_range" | 0.86 | 0.91 | 0.89 | 47 |
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+ | "site" | 0.83 | 0.86| 0.85 | 139 |
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+ | "species" | 0.97 | 1.00 | 0.98 | 59 |
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+ | "structure_element" | 0.91 | 0.92 | 0.91 | 677 |
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+ | "taxonomy_domain" | 0.97 | 0.96 | 0.97 | 73 |
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+
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+
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+ ### Data and annotations
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+
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+ The dataset can be found here: https://huggingface.co/datasets/PDBEurope/protein_structure_NER_model_v1.4