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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...

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Autores principales: 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
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
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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.
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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
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