Reads a PDB file and substitutes b-factor column with hydrophobicity values according to Kyte-Doolittle scale.

If just a PDB file is given as an input, all b-factors will be replaced by respective KD hydrophobicity values. User can also provide a Multiple Sequence Alignment (MSA) in ClustalO format (.aln); hydrophobicity values will be averaged over a corresponding column of the MSA

USAGE: ap_AAHydrophobicity 2gb1.pdb ap_AAHydrophobicity 2gb1.pdb 2gb1.aln 2GB1

The sequence from the given PDB file must also be included in the alignment; its name is third argument of the program.


  • core/chemical/AAHydrophobicity