├── .gitignore ├── LICENSE ├── README.md ├── example ├── alignment │ ├── test │ ├── test_sequence_alignment │ ├── test_sequence_identity │ ├── test_tmalign_alignment │ └── test_tmalign_similarity ├── embedding.pkl ├── pfam_result.json ├── protein.fasta └── structure │ ├── P0AD96 │ ├── P15104 │ ├── P22768 │ ├── P32352 │ └── Q08558 ├── main.ipynb ├── pipeline.ipynb ├── plmsearch ├── __init__.py ├── embedding_generate.py ├── main_pfam.py ├── main_similarity.py ├── pfam_generate.py ├── plmsearch_util │ ├── __init__.py │ ├── alignment_util.py │ ├── model.py │ ├── statistics_util.py │ ├── train_util.py │ └── util.py ├── sequence_align.py ├── tmalign.py └── train.py ├── requirements.sh └── scientist_figures └── workflow_img ├── framework.png ├── framework1.png ├── ss_predictor1.png ├── ss_predictor2.png └── ss_predictor3.png /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/maovshao/PLMSearch/HEAD/.gitignore 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