├── 2_score_filters.xml ├── README.md ├── af_scripts ├── precompute_msas.py ├── predict_from_precomputed.py └── run_alphafold_msaonly.py ├── benchmark.ipynb ├── data ├── human_receptors.csv └── pdb_benchmark_peptides.fasta ├── pdockq.py ├── qc_metrics.py ├── requirements.txt ├── results ├── pdb_benchmark_median.csv └── pdb_benchmark_raw.csv └── score_rosetta.py /2_score_filters.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/2_score_filters.xml -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/README.md -------------------------------------------------------------------------------- /af_scripts/precompute_msas.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/af_scripts/precompute_msas.py -------------------------------------------------------------------------------- /af_scripts/predict_from_precomputed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/af_scripts/predict_from_precomputed.py -------------------------------------------------------------------------------- /af_scripts/run_alphafold_msaonly.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/af_scripts/run_alphafold_msaonly.py -------------------------------------------------------------------------------- /benchmark.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/benchmark.ipynb -------------------------------------------------------------------------------- /data/human_receptors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/data/human_receptors.csv -------------------------------------------------------------------------------- /data/pdb_benchmark_peptides.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/data/pdb_benchmark_peptides.fasta -------------------------------------------------------------------------------- /pdockq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/pdockq.py -------------------------------------------------------------------------------- /qc_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/qc_metrics.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/requirements.txt -------------------------------------------------------------------------------- /results/pdb_benchmark_median.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/results/pdb_benchmark_median.csv -------------------------------------------------------------------------------- /results/pdb_benchmark_raw.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/results/pdb_benchmark_raw.csv -------------------------------------------------------------------------------- /score_rosetta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fteufel/alphafold-peptide-receptors/HEAD/score_rosetta.py --------------------------------------------------------------------------------