The antibiotic'ome search web application takes as input a chemical structure or database of chemical structures in SMILES format, and returns a list of the predicted molecular targets of each user-submitted molecule.

Users can submit a single chemical structure in the text box labeled “Structure.” Alternatively, users can submit a database of chemical structures. This database can be formatted as a text file, with each input SMILES on its own line, e.g.:

CC1=C(N=C(N=C1N)[C@H](CC(=O)N)NC[C@@H](C(=O)N)N)C(=O)N[C@@H](C(C2=CN=CN2)O[C@H]3[C@H]([C@H]([C@@H]([C@@H](O3)CO)O)O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)OC(=O)N)O)C(=O)N[C@H](C)[C@H]([C@H](C)C(=O)N[C@@H]([C@@H](C)O)C(=O)NCCC5=NC(=CS5)C6=NC(=CS6)C(=O)NCCC[S+](C)C)O
CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C@H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@@H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O

Alternatively, users can submit a tab-delimited file with molecule names in the first column and SMILES in the second, e.g.:

BleomycinCC1=C(N=C(N=C1N)[C@H](CC(=O)N)NC[C@@H](C(=O)N)N)C(=O)N[C@@H](C(C2=CN=CN2)O[C@H]3[C@H]([C@H]([C@@H]([C@@H](O3)CO)O)O)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)OC(=O)N)O)C(=O)N[C@H](C)[C@H]([C@H](C)C(=O)N[C@@H]([C@@H](C)O)C(=O)NCCC5=NC(=CS5)C6=NC(=CS6)C(=O)NCCC[S+](C)C)O
ErythromycinCC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@]([C@@H]([C@H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2C[C@@]([C@H]([C@@H](O2)C)O)(C)OC)C)O[C@H]3[C@@H]([C@H](C[C@H](O3)C)N(C)C)O)(C)O)C)C)O)(C)O

The antibiotic'ome search web application generates as output a table which matches input molecules and their SMILES to the single highest-scoring molecular match, the family of compounds to which the top-scoring match belongs, and the molecular target of that family of compounds. Finally, a score is reported corresponding to the confidence of the match.

The antibiotic'ome search web application is a project of the Nathan Magarvey Lab at McMaster University. We aim to provide bio- and chemoinformatic solutions for genomic natural product discovery.

The antibiotic'ome search performs in silico retrobiosynthesis of natural product structures to match them to antibiotics with known molecular targets, in order to computationally predict the targets of user-submitted molecules. It is freely available as an online service for the research community. The antibiotic'ome web application implements the Chemistry Development Kit¹ and the Needleman-Wunsch algorithm².

¹ Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E. and Willighagen, E. (2003) The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. J. Chem. Inf. Comput. Sci., 43, 493-500.

² Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-53.

The Magarvey Lab does not warrant or assume any legal responsibility for the accuracy, completeness, or usefulness of any information generated by the software available from this server.

The Magarvey Lab does not collect data or personal information for purposes other than executing the analytical software from this server. All data submitted to the server will be securely stored for use with the Antibiotic'ome software package only. To prevent unauthorised disclosure or access to your data and information, we have implemented strong physical and electronic security safeguards.

This website's policies and disclaimers were updated on October 8th, 2015.