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rBAN: retro-biosynthetic analysis of nonribosomal peptides
Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks of nonribsosomal peptides (NRPs) and as such may give insight into the origin, biosynthesis and bioactivities of their constitutive peptides. Hence, the structural representation of NRPs usin...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689883/ https://www.ncbi.nlm.nih.gov/pubmed/30737579 http://dx.doi.org/10.1186/s13321-019-0335-x |
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author | Ricart, Emma Leclère, Valérie Flissi, Areski Mueller, Markus Pupin, Maude Lisacek, Frédérique |
author_facet | Ricart, Emma Leclère, Valérie Flissi, Areski Mueller, Markus Pupin, Maude Lisacek, Frédérique |
author_sort | Ricart, Emma |
collection | PubMed |
description | Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks of nonribsosomal peptides (NRPs) and as such may give insight into the origin, biosynthesis and bioactivities of their constitutive peptides. Hence, the structural representation of NRPs using monomers provides a biologically interesting skeleton of these secondary metabolites. Databases dedicated to NRPs such as Norine, already integrate monomer-based annotations in order to facilitate the development of structural analysis tools. In this paper, we present rBAN (retro-biosynthetic analysis of nonribosomal peptides), a new computational tool designed to predict the monomeric graph of NRPs from their atomic structure in SMILES format. This prediction is achieved through the “in silico” fragmentation of a chemical structure and matching the resulting fragments against the monomers of Norine for identification. Structures containing monomers not yet recorded in Norine, are processed in a “discovery mode” that uses the RESTful service from PubChem to search the unidentified substructures and suggest new monomers. rBAN was integrated in a pipeline for the curation of Norine data in which it was used to check the correspondence between the monomeric graphs annotated in Norine and SMILES-predicted graphs. The process concluded with the validation of the 97.26% of the records in Norine, a two-fold extension of its SMILES data and the introduction of 11 new monomers suggested in the discovery mode. The accuracy, robustness and high-performance of rBAN were demonstrated in benchmarking it against other tools with the same functionality: Smiles2Monomers and GRAPE. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13321-019-0335-x) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6689883 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-66898832019-08-15 rBAN: retro-biosynthetic analysis of nonribosomal peptides Ricart, Emma Leclère, Valérie Flissi, Areski Mueller, Markus Pupin, Maude Lisacek, Frédérique J Cheminform Research Article Proteinogenic and non-proteinogenic amino acids, fatty acids or glycans are some of the main building blocks of nonribsosomal peptides (NRPs) and as such may give insight into the origin, biosynthesis and bioactivities of their constitutive peptides. Hence, the structural representation of NRPs using monomers provides a biologically interesting skeleton of these secondary metabolites. Databases dedicated to NRPs such as Norine, already integrate monomer-based annotations in order to facilitate the development of structural analysis tools. In this paper, we present rBAN (retro-biosynthetic analysis of nonribosomal peptides), a new computational tool designed to predict the monomeric graph of NRPs from their atomic structure in SMILES format. This prediction is achieved through the “in silico” fragmentation of a chemical structure and matching the resulting fragments against the monomers of Norine for identification. Structures containing monomers not yet recorded in Norine, are processed in a “discovery mode” that uses the RESTful service from PubChem to search the unidentified substructures and suggest new monomers. rBAN was integrated in a pipeline for the curation of Norine data in which it was used to check the correspondence between the monomeric graphs annotated in Norine and SMILES-predicted graphs. The process concluded with the validation of the 97.26% of the records in Norine, a two-fold extension of its SMILES data and the introduction of 11 new monomers suggested in the discovery mode. The accuracy, robustness and high-performance of rBAN were demonstrated in benchmarking it against other tools with the same functionality: Smiles2Monomers and GRAPE. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13321-019-0335-x) contains supplementary material, which is available to authorized users. Springer International Publishing 2019-02-08 /pmc/articles/PMC6689883/ /pubmed/30737579 http://dx.doi.org/10.1186/s13321-019-0335-x Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Ricart, Emma Leclère, Valérie Flissi, Areski Mueller, Markus Pupin, Maude Lisacek, Frédérique rBAN: retro-biosynthetic analysis of nonribosomal peptides |
title | rBAN: retro-biosynthetic analysis of nonribosomal peptides |
title_full | rBAN: retro-biosynthetic analysis of nonribosomal peptides |
title_fullStr | rBAN: retro-biosynthetic analysis of nonribosomal peptides |
title_full_unstemmed | rBAN: retro-biosynthetic analysis of nonribosomal peptides |
title_short | rBAN: retro-biosynthetic analysis of nonribosomal peptides |
title_sort | rban: retro-biosynthetic analysis of nonribosomal peptides |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689883/ https://www.ncbi.nlm.nih.gov/pubmed/30737579 http://dx.doi.org/10.1186/s13321-019-0335-x |
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