PepSift

Summary

Identify peptides and their derivatives from small molecule datasets.

Installation

pip install pepsift

Usage

PepSift relies on multiple criteria defining different types od amino acids and polymers thereof.

There are currently 5 different levels available from most to least stringent:

level	description	comment
SiftLevel.NaturalLAminoAcids	natural L-amino acids and peptides thereof	e.g. identify L-Alanine or the sequence ACDEFGHIKLMNPQRSTVWY
SiftLevel.NaturalLDAminoAcids	natural L- and D-amino acid and peptides thereof	e.g. identify L-Alanine or the sequences D-A L-W, L-H D-Q, D-M D-K
SiftLevel.NaturalAminoAcidDerivatives	derivatives of natural L- and D-amino acid and peptides thereof	i.e. any compound containing a canonical amino acid/peptide backbone
SiftLevel.NonNaturalAminoAcidDerivatives	non-natural amino acid derivatives and peptides thereof	e.g. identify beta-homo-alanine or alpha-methyl-Tyr
SiftLevel.AllAmineAndAcid	compounds containing amine and carboxylic acid moieties	e.g. 3-[3-(2-Aminoethyl)cyclohexyl]propionic acid

These levels allow for granular selection of different types amino acids/peptides.

The decreasing stringency of `SiftLevel` criteria is exemplified below.

from pepsift import PepSift, SiftLevel

from rdkit import Chem

ps1 = PepSift(SiftLevel.NaturalLAminoAcids)
ps2 = PepSift(SiftLevel.NaturalLDAminoAcids)
ps3 = PepSift(SiftLevel.NaturalAminoAcidDerivatives)
ps4 = PepSift(SiftLevel.NonNaturalAminoAcidDerivatives)
ps5 = PepSift(SiftLevel.AllAmineAndAcid)

mols = [Chem.MolFromSmiles('C[C@@H](C(=O)O)N'),  # L-Ala
        Chem.MolFromSmiles('C[C@H](C(=O)O)N'),   # D-Ala
        Chem.MolFromSmiles('C[C@@H](CN)C(=O)O'), # Beta-homo-Ala
        Chem.MolFromSmiles('CC(C)(C(=O)O)N'),    # Alpha-methyl-Ala
        Chem.MolFromSmiles('NCCCCCCCCCCCCCCCC(=O)O'),   # Amino-hexadecanoic acid
        Chem.MolFromSmiles('c1ccccc1'),           # Benzene
       ]

for mol in mols:
    print((ps1.is_peptide(mol),
           ps2.is_peptide(mol),
           ps3.is_peptide(mol),
           ps4.is_peptide(mol),
           ps5.is_peptide(mol)
           )
          )

# L-Ala
# (True, True, True, True, True)
# D-Ala
# (False, True, True, True, True)
# Beta-homo-Ala
# (False, False, True, True, True)
# Alpha-methyl-Ala
# (False, False, False, True, True)
# Amino-hexadecanoic acid
# (False, False, False, False, True)
# Benzene
# (False, False, False, False, False)

:warning: Any peptide containing a natural amino acid is considered a derivative of natural amino acids (even if it also contains non natural amino acids)