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

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 i...

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Detalles Bibliográficos
Autores principales: Minkiewicz, Piotr, Iwaniak, Anna, Darewicz, Małgorzata
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6149970/
https://www.ncbi.nlm.nih.gov/pubmed/29186902
http://dx.doi.org/10.3390/molecules22122075
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author Minkiewicz, Piotr
Iwaniak, Anna
Darewicz, Małgorzata
author_facet Minkiewicz, Piotr
Iwaniak, Anna
Darewicz, Małgorzata
author_sort Minkiewicz, Piotr
collection PubMed
description 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.
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spelling pubmed-61499702018-11-13 Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions Minkiewicz, Piotr Iwaniak, Anna Darewicz, Małgorzata Molecules Review 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. MDPI 2017-11-27 /pmc/articles/PMC6149970/ /pubmed/29186902 http://dx.doi.org/10.3390/molecules22122075 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Minkiewicz, Piotr
Iwaniak, Anna
Darewicz, Małgorzata
Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions
title Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions
title_full Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions
title_fullStr Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions
title_full_unstemmed Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions
title_short Annotation of Peptide Structures Using SMILES and Other Chemical Codes–Practical Solutions
title_sort annotation of peptide structures using smiles and other chemical codes–practical solutions
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6149970/
https://www.ncbi.nlm.nih.gov/pubmed/29186902
http://dx.doi.org/10.3390/molecules22122075
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