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update guides to use sdk and v3 standards #8

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Merged
nsh87 merged 1 commit into from
Jul 1, 2025
Merged

update guides to use sdk and v3 standards #8

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341 changes: 205 additions & 136 deletions content/0_Introduction.ipynb
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226 changes: 144 additions & 82 deletions content/1.0_ESMFold.ipynb
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375 changes: 153 additions & 222 deletions content/1.1_ESMFold_PDB_Generation.ipynb
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3,789 changes: 2,438 additions & 1,351 deletions content/2.0_ESM2.ipynb
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42,682 changes: 171 additions & 42,511 deletions content/2.1_ESM2_Attention_Map.ipynb
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71,875 changes: 172 additions & 71,703 deletions content/2.2_ESM2_Protein_Contact_Map.ipynb
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187,330 changes: 71,844 additions & 115,486 deletions content/2.3_ESM2_Embeddings_XGBoost.ipynb
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608 changes: 541 additions & 67 deletions content/3.0_ESM_1v.ipynb
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2,026 changes: 1,585 additions & 441 deletions content/3.1_ESM-1v_Deep_Mutational_Scan_Protein.ipynb
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257 changes: 163 additions & 94 deletions content/4.0_ESM-IF1.ipynb
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145 changes: 0 additions & 145 deletions content/5.0_ProteInfer.ipynb
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