CHUCKLES: a method for representing and searching peptide and peptoid sequences on both monomer and atomic levels.
Dual representation of peptide and non-peptide structures in a chemical database as atomic-level molecular graphs and sequence strings permits chemical substructure and similarity searches as well as sequence-based substring and regular expression searches. CHUCKLES interconverts monomer-based sequences with SMILES, which represent atomic-level molecular graphs. Forward-translation maps peptide or other sequences into SMILES. Back-translation extracts monomer sequences from SMILES. This approach permits a generalized representation of monomers allowing user specification of any monomer. CHUCKLES allows mixing of atoms with user-defined monomer names; that is, monomer representation is consistent with SMILES notation. In addition, oligomer branching and cyclization are handled.
Siani
M A
MA
Chiron Corporation, Emeryville, California 94608.
Weininger
D
D
Blaney
J M
JM
D000595:Amino Acid Sequence; D016208:Databases, Factual; D005069:Evaluation Studies as Topic; D007328:Insulin / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry* / Q000235:genetics; D034444:Peptoids; D012984:Software; D012985:Software Design
D007328:Insulin; D010455:Peptides; D034444:Peptoids