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Molecules 2017, 22(12), 2075; doi:10.3390/molecules22122075

Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions

Department of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, 10-726 Olsztyn-Kortowo, Poland
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Received: 16 October 2017 / Revised: 15 November 2017 / Accepted: 25 November 2017 / Published: 27 November 2017
(This article belongs to the Section Bioorganic Chemistry)
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Abstract

Contemporary peptide science exploits methods and tools of bioinformatics, and cheminformatics. These approaches use different languages to describe peptide structures—amino acid sequences and chemical codes (especially SMILES), respectively. The latter may be applied, e.g., in comparative studies involving structures and properties of peptides and peptidomimetics. Progress in peptide science “in silico” may be achieved via better communication between biologists and chemists, involving the translation of peptide representation from amino acid sequence into SMILES code. Recent recommendations concerning good practice in chemical information include careful verification of data and their annotation. This publication discusses the generation of SMILES representations of peptides using existing software. Construction of peptide structures containing unnatural and modified amino acids (with special attention paid on glycosylated peptides) is also included. Special attention is paid to the detection and correction of typical errors occurring in SMILES representations of peptides and their correction using molecular editors. Brief recommendations for training of staff working on peptide annotations, are discussed as well. View Full-Text
Keywords: peptides; glycopeptides; chemical modifications; bioinformatics; cheminformatics; chemical information; good practice; molecular editors; SMILES code peptides; glycopeptides; chemical modifications; bioinformatics; cheminformatics; chemical information; good practice; molecular editors; SMILES code
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Minkiewicz, P.; Iwaniak, A.; Darewicz, M. Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions. Molecules 2017, 22, 2075.

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