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PEPCONF, a diverse data set of peptide conformational energies
We present an extensive and diverse database of peptide conformational energies. Our database contains five different classes of model geometries: dipeptides, tripeptides, and disulfide-bridged, bioactive, and cyclic peptides. In total, the database consists of 3775 conformational energy data points...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343515/ https://www.ncbi.nlm.nih.gov/pubmed/30667382 http://dx.doi.org/10.1038/sdata.2018.310 |
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author | Prasad, Viki Kumar Otero-de-la-Roza, Alberto DiLabio, Gino A. |
author_facet | Prasad, Viki Kumar Otero-de-la-Roza, Alberto DiLabio, Gino A. |
author_sort | Prasad, Viki Kumar |
collection | PubMed |
description | We present an extensive and diverse database of peptide conformational energies. Our database contains five different classes of model geometries: dipeptides, tripeptides, and disulfide-bridged, bioactive, and cyclic peptides. In total, the database consists of 3775 conformational energy data points and 4530 conformer geometries. All the reference energies have been calculated at the LC-ωPBE-XDM/aug-cc-pVTZ level of theory, which is shown to yield conformational energies with an accuracy in the order of tenths of a kcal/mol when compared to complete-basis-set coupled-cluster reference data. The peptide conformational data set (PEPCONF) is presented as a high-quality reference set for the development and benchmarking of molecular-mechanics and semi-empirical electronic structure methods, which are the most commonly used techniques in the modeling of medium to large proteins. |
format | Online Article Text |
id | pubmed-6343515 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-63435152019-01-24 PEPCONF, a diverse data set of peptide conformational energies Prasad, Viki Kumar Otero-de-la-Roza, Alberto DiLabio, Gino A. Sci Data Data Descriptor We present an extensive and diverse database of peptide conformational energies. Our database contains five different classes of model geometries: dipeptides, tripeptides, and disulfide-bridged, bioactive, and cyclic peptides. In total, the database consists of 3775 conformational energy data points and 4530 conformer geometries. All the reference energies have been calculated at the LC-ωPBE-XDM/aug-cc-pVTZ level of theory, which is shown to yield conformational energies with an accuracy in the order of tenths of a kcal/mol when compared to complete-basis-set coupled-cluster reference data. The peptide conformational data set (PEPCONF) is presented as a high-quality reference set for the development and benchmarking of molecular-mechanics and semi-empirical electronic structure methods, which are the most commonly used techniques in the modeling of medium to large proteins. Nature Publishing Group 2019-01-22 /pmc/articles/PMC6343515/ /pubmed/30667382 http://dx.doi.org/10.1038/sdata.2018.310 Text en Copyright © 2019, The Author(s) http://creativecommons.org/licenses/by/4.0/ Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article. |
spellingShingle | Data Descriptor Prasad, Viki Kumar Otero-de-la-Roza, Alberto DiLabio, Gino A. PEPCONF, a diverse data set of peptide conformational energies |
title | PEPCONF, a diverse data set of peptide conformational energies |
title_full | PEPCONF, a diverse data set of peptide conformational energies |
title_fullStr | PEPCONF, a diverse data set of peptide conformational energies |
title_full_unstemmed | PEPCONF, a diverse data set of peptide conformational energies |
title_short | PEPCONF, a diverse data set of peptide conformational energies |
title_sort | pepconf, a diverse data set of peptide conformational energies |
topic | Data Descriptor |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343515/ https://www.ncbi.nlm.nih.gov/pubmed/30667382 http://dx.doi.org/10.1038/sdata.2018.310 |
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