Cargando…
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy
Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure composition of proteins. To derive accurate and detailed structural information from the CD spectra, we have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which can handle the sp...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252784/ https://www.ncbi.nlm.nih.gov/pubmed/35544232 http://dx.doi.org/10.1093/nar/gkac345 |
_version_ | 1784740347636613120 |
---|---|
author | Micsonai, András Moussong, Éva Wien, Frank Boros, Eszter Vadászi, Henrietta Murvai, Nikoletta Lee, Young-Ho Molnár, Tamás Réfrégiers, Matthieu Goto, Yuji Tantos, Ágnes Kardos, József |
author_facet | Micsonai, András Moussong, Éva Wien, Frank Boros, Eszter Vadászi, Henrietta Murvai, Nikoletta Lee, Young-Ho Molnár, Tamás Réfrégiers, Matthieu Goto, Yuji Tantos, Ágnes Kardos, József |
author_sort | Micsonai, András |
collection | PubMed |
description | Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure composition of proteins. To derive accurate and detailed structural information from the CD spectra, we have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which can handle the spectral diversity of β-structured proteins. The BeStSel webserver provides this method with useful accessories to the community with the main goal to analyze single or multiple protein CD spectra. Uniquely, BeStSel provides information on eight secondary structure components including parallel β-structure and antiparallel β-sheets with three different groups of twist. It overperforms any available method in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification. A new module of the webserver helps to distinguish intrinsically disordered proteins by their CD spectrum. Secondary structure calculation for uploaded PDB files will help the experimental verification of protein MD and in silico modelling using CD spectroscopy. The server also calculates extinction coefficients from the primary sequence for CD users to determine the accurate protein concentrations which is a prerequisite for reliable secondary structure determination. The BeStSel server can be freely accessed at https://bestsel.elte.hu. |
format | Online Article Text |
id | pubmed-9252784 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-92527842022-07-05 BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy Micsonai, András Moussong, Éva Wien, Frank Boros, Eszter Vadászi, Henrietta Murvai, Nikoletta Lee, Young-Ho Molnár, Tamás Réfrégiers, Matthieu Goto, Yuji Tantos, Ágnes Kardos, József Nucleic Acids Res Web Server Issue Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure composition of proteins. To derive accurate and detailed structural information from the CD spectra, we have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which can handle the spectral diversity of β-structured proteins. The BeStSel webserver provides this method with useful accessories to the community with the main goal to analyze single or multiple protein CD spectra. Uniquely, BeStSel provides information on eight secondary structure components including parallel β-structure and antiparallel β-sheets with three different groups of twist. It overperforms any available method in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification. A new module of the webserver helps to distinguish intrinsically disordered proteins by their CD spectrum. Secondary structure calculation for uploaded PDB files will help the experimental verification of protein MD and in silico modelling using CD spectroscopy. The server also calculates extinction coefficients from the primary sequence for CD users to determine the accurate protein concentrations which is a prerequisite for reliable secondary structure determination. The BeStSel server can be freely accessed at https://bestsel.elte.hu. Oxford University Press 2022-05-11 /pmc/articles/PMC9252784/ /pubmed/35544232 http://dx.doi.org/10.1093/nar/gkac345 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Web Server Issue Micsonai, András Moussong, Éva Wien, Frank Boros, Eszter Vadászi, Henrietta Murvai, Nikoletta Lee, Young-Ho Molnár, Tamás Réfrégiers, Matthieu Goto, Yuji Tantos, Ágnes Kardos, József BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy |
title | BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy |
title_full | BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy |
title_fullStr | BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy |
title_full_unstemmed | BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy |
title_short | BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy |
title_sort | bestsel: webserver for secondary structure and fold prediction for protein cd spectroscopy |
topic | Web Server Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252784/ https://www.ncbi.nlm.nih.gov/pubmed/35544232 http://dx.doi.org/10.1093/nar/gkac345 |
work_keys_str_mv | AT micsonaiandras bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT moussongeva bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT wienfrank bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT boroseszter bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT vadaszihenrietta bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT murvainikoletta bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT leeyoungho bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT molnartamas bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT refregiersmatthieu bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT gotoyuji bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT tantosagnes bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy AT kardosjozsef bestselwebserverforsecondarystructureandfoldpredictionforproteincdspectroscopy |