pdb_canonical: converting modified aminoacids to their standard counterparts

JoaoRodrigues commented 5 years ago

Is your tool request related to a problem? Please describe. PDB files often have modified/nonstandard residues (e.g. MSE) that are labeled as HETATM in the middle of the sequence. These are not accepted by many modeling tools.

Describe the solution you'd like It would be interesting to have a tool to replace them by the canonical versions (e.g. MSE -> MET) and remove the extra atoms.

Does any of the existing tools or a combination of them do what you want? No.

amjjbonvin commented 5 years ago

No need to delete atoms for the MSE to MET change. Simply rename the SE atom to SD

JoaoRodrigues commented 5 years ago

What about every other nonstandard aminoacid? Not to mention that bond length, angles, etc, might be quite different. I'd advocate a more general solution: remove atoms that do not match the "standard" template.

amjjbonvin commented 5 years ago

Let's then first make a list of such non-standard amino acids... For MSE to MET, it really doesn't make sense to delete the SE. But anyway a proper soft should be able to rebuild the missing bits.

amjjbonvin commented 5 years ago

Probably a good start for such a list are:

JoaoRodrigues commented 5 years ago

I lifted this off pdbfixer, which would be a good list to start with as well:

substitutions = {
    '2AS':'ASP', '3AH':'HIS', '5HP':'GLU', 'ACL':'ARG', 'AGM':'ARG', 'AIB':'ALA', 'ALM':'ALA', 'ALO':'THR', 'ALY':'LYS', 'ARM':'ARG',
    'ASA':'ASP', 'ASB':'ASP', 'ASK':'ASP', 'ASL':'ASP', 'ASQ':'ASP', 'AYA':'ALA', 'BCS':'CYS', 'BHD':'ASP', 'BMT':'THR', 'BNN':'ALA',
    'BUC':'CYS', 'BUG':'LEU', 'C5C':'CYS', 'C6C':'CYS', 'CAS':'CYS', 'CCS':'CYS', 'CEA':'CYS', 'CGU':'GLU', 'CHG':'ALA', 'CLE':'LEU', 'CME':'CYS',
    'CSD':'ALA', 'CSO':'CYS', 'CSP':'CYS', 'CSS':'CYS', 'CSW':'CYS', 'CSX':'CYS', 'CXM':'MET', 'CY1':'CYS', 'CY3':'CYS', 'CYG':'CYS',
    'CYM':'CYS', 'CYQ':'CYS', 'DAH':'PHE', 'DAL':'ALA', 'DAR':'ARG', 'DAS':'ASP', 'DCY':'CYS', 'DGL':'GLU', 'DGN':'GLN', 'DHA':'ALA',
    'DHI':'HIS', 'DIL':'ILE', 'DIV':'VAL', 'DLE':'LEU', 'DLY':'LYS', 'DNP':'ALA', 'DPN':'PHE', 'DPR':'PRO', 'DSN':'SER', 'DSP':'ASP',
    'DTH':'THR', 'DTR':'TRP', 'DTY':'TYR', 'DVA':'VAL', 'EFC':'CYS', 'FLA':'ALA', 'FME':'MET', 'GGL':'GLU', 'GL3':'GLY', 'GLZ':'GLY',
    'GMA':'GLU', 'GSC':'GLY', 'HAC':'ALA', 'HAR':'ARG', 'HIC':'HIS', 'HIP':'HIS', 'HMR':'ARG', 'HPQ':'PHE', 'HTR':'TRP', 'HYP':'PRO',
    'IAS':'ASP', 'IIL':'ILE', 'IYR':'TYR', 'KCX':'LYS', 'LLP':'LYS', 'LLY':'LYS', 'LTR':'TRP', 'LYM':'LYS', 'LYZ':'LYS', 'MAA':'ALA', 'MEN':'ASN',
    'MHS':'HIS', 'MIS':'SER', 'MLE':'LEU', 'MPQ':'GLY', 'MSA':'GLY', 'MSE':'MET', 'MVA':'VAL', 'NEM':'HIS', 'NEP':'HIS', 'NLE':'LEU',
    'NLN':'LEU', 'NLP':'LEU', 'NMC':'GLY', 'OAS':'SER', 'OCS':'CYS', 'OMT':'MET', 'PAQ':'TYR', 'PCA':'GLU', 'PEC':'CYS', 'PHI':'PHE',
    'PHL':'PHE', 'PR3':'CYS', 'PRR':'ALA', 'PTR':'TYR', 'PYX':'CYS', 'SAC':'SER', 'SAR':'GLY', 'SCH':'CYS', 'SCS':'CYS', 'SCY':'CYS',
    'SEL':'SER', 'SEP':'SER', 'SET':'SER', 'SHC':'CYS', 'SHR':'LYS', 'SMC':'CYS', 'SOC':'CYS', 'STY':'TYR', 'SVA':'SER', 'TIH':'ALA',
    'TPL':'TRP', 'TPO':'THR', 'TPQ':'ALA', 'TRG':'LYS', 'TRO':'TRP', 'TYB':'TYR', 'TYI':'TYR', 'TYQ':'TYR', 'TYS':'TYR', 'TYY':'TYR'
}

JoaoRodrigues commented 4 years ago

I'll define this as out of scope for now. It'd be tough to maintain a list of conversions, better left to specialized tools.

haddocking / pdb-tools

pdb_canonical: converting modified aminoacids to their standard counterparts #23