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ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins
We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662583/ https://www.ncbi.nlm.nih.gov/pubmed/26623185 http://dx.doi.org/10.7717/peerj.1344 |
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author | Larsen, Anders S. Bratholm, Lars A. Christensen, Anders S. Channir, Maher Jensen, Jan H. |
author_facet | Larsen, Anders S. Bratholm, Lars A. Christensen, Anders S. Channir, Maher Jensen, Jan H. |
author_sort | Larsen, Anders S. |
collection | PubMed |
description | We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. |
format | Online Article Text |
id | pubmed-4662583 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-46625832015-11-30 ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins Larsen, Anders S. Bratholm, Lars A. Christensen, Anders S. Channir, Maher Jensen, Jan H. PeerJ Biophysics We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. PeerJ Inc. 2015-10-20 /pmc/articles/PMC4662583/ /pubmed/26623185 http://dx.doi.org/10.7717/peerj.1344 Text en © 2015 Larsen et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Biophysics Larsen, Anders S. Bratholm, Lars A. Christensen, Anders S. Channir, Maher Jensen, Jan H. ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins |
title | ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins |
title_full | ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins |
title_fullStr | ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins |
title_full_unstemmed | ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins |
title_short | ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins |
title_sort | procs15: a dft-based chemical shift predictor for backbone and cβ atoms in proteins |
topic | Biophysics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4662583/ https://www.ncbi.nlm.nih.gov/pubmed/26623185 http://dx.doi.org/10.7717/peerj.1344 |
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