VLPIM Tool setup

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ProteinMPNN
  • pdb_path: path to reference structure PDB.
  • epitope_df: DataFrame with columns sequence,start,end,score,method.
  • samples_per_temp: sequences per temperature (default 20).
  • temps: sampling temperatures (default [0.1, 0.3, 0.5]).
NetMHCIIpan
  • fasta_path: FASTA file path.
  • HLA_alleles: e.g., DRB1*01:01, DRB1*03:01, DRB1*04:01, DRB1*07:01, DRB1*08:01, DRB1*11:01, DRB1*13:01, DRB1*15:01
  • Fixed flags: -length 15, -BA, -rank, version 4.3.
AlphaFold3
  • seeds: user-provided or automatically generated seeds.
  • max_candidates: limit number of sequences (default 10).
Rosetta Interface Analyzer
  • analyze_interface(pdb_path, output_dir): returns dG/dSASA, packstat, delta_unsat_hbonds.
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