Open Access
Nucleic Acids Research, volume 43, issue W1, pages W370-W377
CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts
1
Department of Computing Science University of Alberta Edmonton, AB, T6G 2E8, Canada
|
2
Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
|
Publication type: Journal Article
Publication date: 2015-05-15
Journal:
Nucleic Acids Research
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 14.9
ISSN: 03051048, 13624962
PubMed ID:
25979265
Genetics
Abstract
The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I′, II′ and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.
Citations by journals
|
5
10
15
20
25
30
|
|
|
Biomolecular NMR Assignments
|
Biomolecular NMR Assignments
28 publications, 22.4%
|
|
Journal of Biomolecular NMR
|
Journal of Biomolecular NMR
7 publications, 5.6%
|
|
Biochemistry
|
Biochemistry
6 publications, 4.8%
|
|
Nature Communications
|
Nature Communications
5 publications, 4%
|
|
Scientific Reports
|
Scientific Reports
5 publications, 4%
|
|
Biophysical Journal
|
Biophysical Journal
3 publications, 2.4%
|
|
International Journal of Biological Macromolecules
|
International Journal of Biological Macromolecules
3 publications, 2.4%
|
|
Structure
|
Structure
3 publications, 2.4%
|
|
Journal of Biological Chemistry
|
Journal of Biological Chemistry
3 publications, 2.4%
|
|
Journal of Molecular Biology
|
Journal of Molecular Biology
3 publications, 2.4%
|
|
International Journal of Molecular Sciences
|
International Journal of Molecular Sciences
2 publications, 1.6%
|
|
PLoS ONE
|
PLoS ONE
2 publications, 1.6%
|
|
Protein Science
|
Protein Science
2 publications, 1.6%
|
|
ChemBioChem
|
ChemBioChem
2 publications, 1.6%
|
|
Angewandte Chemie
|
Angewandte Chemie
2 publications, 1.6%
|
|
Angewandte Chemie - International Edition
|
Angewandte Chemie - International Edition
2 publications, 1.6%
|
|
Journal of Physical Chemistry B
|
Journal of Physical Chemistry B
2 publications, 1.6%
|
|
Science advances
|
Science advances
2 publications, 1.6%
|
|
eLife
|
eLife
2 publications, 1.6%
|
|
Methods in Enzymology
|
Methods in Enzymology
2 publications, 1.6%
|
|
Protein and Peptide Letters
|
Protein and Peptide Letters
1 publication, 0.8%
|
|
Current Medicinal Chemistry
|
Current Medicinal Chemistry
1 publication, 0.8%
|
|
Current Bioinformatics
|
Current Bioinformatics
1 publication, 0.8%
|
|
Molecules
|
Molecules
1 publication, 0.8%
|
|
Frontiers in Molecular Biosciences
|
Frontiers in Molecular Biosciences
1 publication, 0.8%
|
|
Nature Chemical Biology
|
Nature Chemical Biology
1 publication, 0.8%
|
|
Cellular and Molecular Life Sciences
|
Cellular and Molecular Life Sciences
1 publication, 0.8%
|
|
RSC Advances
|
RSC Advances
1 publication, 0.8%
|
|
Toxicon
|
Toxicon
1 publication, 0.8%
|
|
5
10
15
20
25
30
|
Citations by publishers
|
5
10
15
20
25
30
35
40
45
50
|
|
|
Springer Nature
|
Springer Nature
49 publications, 39.2%
|
|
Elsevier
|
Elsevier
17 publications, 13.6%
|
|
Wiley
|
Wiley
11 publications, 8.8%
|
|
American Chemical Society (ACS)
|
American Chemical Society (ACS)
10 publications, 8%
|
|
Multidisciplinary Digital Publishing Institute (MDPI)
|
Multidisciplinary Digital Publishing Institute (MDPI)
4 publications, 3.2%
|
|
Bentham Science
|
Bentham Science
3 publications, 2.4%
|
|
Biophysical Society
|
Biophysical Society
3 publications, 2.4%
|
|
American Society for Biochemistry and Molecular Biology
|
American Society for Biochemistry and Molecular Biology
3 publications, 2.4%
|
|
Public Library of Science (PLoS)
|
Public Library of Science (PLoS)
2 publications, 1.6%
|
|
American Association for the Advancement of Science (AAAS)
|
American Association for the Advancement of Science (AAAS)
2 publications, 1.6%
|
|
eLife Sciences Publications
|
eLife Sciences Publications
2 publications, 1.6%
|
|
Frontiers Media S.A.
|
Frontiers Media S.A.
1 publication, 0.8%
|
|
Royal Society of Chemistry (RSC)
|
Royal Society of Chemistry (RSC)
1 publication, 0.8%
|
|
Oxford University Press
|
Oxford University Press
1 publication, 0.8%
|
|
Walter de Gruyter
|
Walter de Gruyter
1 publication, 0.8%
|
|
American Society for Microbiology
|
American Society for Microbiology
1 publication, 0.8%
|
|
Proceedings of the National Academy of Sciences (PNAS)
|
Proceedings of the National Academy of Sciences (PNAS)
1 publication, 0.8%
|
|
Cold Spring Harbor Laboratory
|
Cold Spring Harbor Laboratory
1 publication, 0.8%
|
|
5
10
15
20
25
30
35
40
45
50
|
- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
{"yearsCitations":{"type":"bar","data":{"show":true,"labels":[2016,2017,2018,2019,2020,2021,2022,2023,2024],"ids":[0,0,0,0,0,0,0,0,0],"codes":[0,0,0,0,0,0,0,0,0],"imageUrls":["","","","","","","","",""],"datasets":[{"label":"Citations number","data":[8,14,21,16,20,22,11,12,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":["6.4","11.2","16.8","12.8","16","17.6","8.8","9.6","0.8"],"barThickness":null}]},"options":{"indexAxis":"x","maintainAspectRatio":true,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":1,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Citations per year","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"journals":{"type":"bar","data":{"show":true,"labels":["Biomolecular NMR Assignments","Journal of Biomolecular NMR","Biochemistry","Nature Communications","Scientific Reports","Biophysical Journal","International Journal of Biological Macromolecules","Structure","Journal of Biological Chemistry","Journal of Molecular Biology","International Journal of Molecular Sciences","PLoS ONE","Protein Science","ChemBioChem","Angewandte Chemie","Angewandte Chemie - International Edition","Journal of Physical Chemistry B","Science advances","eLife","Methods in Enzymology","Protein and Peptide Letters","Current Medicinal Chemistry","Current Bioinformatics","Molecules","Frontiers in Molecular Biosciences","Nature Chemical Biology","Cellular and Molecular Life Sciences","RSC Advances","Toxicon"],"ids":[15938,21752,9964,3231,13767,4026,23035,5828,19451,19701,14627,24963,2646,12154,25450,19215,14990,23003,24138,24566,11667,17087,15773,1770,3133,17718,5151,3100,13716],"codes":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/Bmz9XNb2QDptmPTa5N8huM54tShVewUj8fZqKFRy_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/OuA6WPZekwEiUM99mP2pSqj4yHPxHezM6xgLhAjO_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/PRGhlgB4OKRltSNtT39eA6wlnOTGRap1QQ6FQHih_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/s10mcsCV4OAUg9O2KrqOquQC0PhyLMI8hUUkuflM_medium.webp","\/storage\/images\/resized\/eIZgkq1MRZyJ3hBkdupnUUv7wgB6zCl9D99SlPN5_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/doUaFUZdxUEQjLi1TwZjGHi8HXYNWWSk04dSC6Xh_medium.webp","\/storage\/images\/resized\/doUaFUZdxUEQjLi1TwZjGHi8HXYNWWSk04dSC6Xh_medium.webp","\/storage\/images\/resized\/doUaFUZdxUEQjLi1TwZjGHi8HXYNWWSk04dSC6Xh_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp"],"datasets":[{"label":"","data":[28,7,6,5,5,3,3,3,3,3,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[22.4,5.6,4.8,4,4,2.4,2.4,2.4,2.4,2.4,1.6,1.6,1.6,1.6,1.6,1.6,1.6,1.6,1.6,1.6,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8,0.8],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Journals","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}},"publishers":{"type":"bar","data":{"show":true,"labels":["Springer Nature","Elsevier","Wiley","American Chemical Society (ACS)","Multidisciplinary Digital Publishing Institute (MDPI)","Bentham Science","Biophysical Society","American Society for Biochemistry and Molecular Biology","Public Library of Science (PLoS)","American Association for the Advancement of Science (AAAS)","eLife Sciences Publications","Frontiers Media S.A.","Royal Society of Chemistry (RSC)","Oxford University Press","Walter de Gruyter","American Society for Microbiology","Proceedings of the National Academy of Sciences (PNAS)","Cold Spring Harbor Laboratory"],"ids":[8,17,11,40,202,39,1454,2090,344,189,6627,208,123,19,4,142,162,6909],"codes":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"imageUrls":["\/storage\/images\/resized\/voXLqlsvTwv5p3iMQ8Dhs95nqB4AXOG7Taj7G4ra_medium.webp","\/storage\/images\/resized\/GDnYOu1UpMMfMMRV6Aqle4H0YLLsraeD9IP9qScG_medium.webp","\/storage\/images\/resized\/bRyGpdm98BkAUYiK1YFNpl5Z7hPu6Gd87gbIeuG3_medium.webp","\/storage\/images\/resized\/iLiQsFqFaSEx6chlGQ5fbAwF6VYU3WWa08hkss0g_medium.webp","\/storage\/images\/resized\/MjH1ITP7lMYGxeqUZfkt2BnVLgjkk413jwBV97XX_medium.webp","\/storage\/images\/resized\/doUaFUZdxUEQjLi1TwZjGHi8HXYNWWSk04dSC6Xh_medium.webp","\/storage\/images\/resized\/Bmz9XNb2QDptmPTa5N8huM54tShVewUj8fZqKFRy_medium.webp","\/storage\/images\/resized\/OuA6WPZekwEiUM99mP2pSqj4yHPxHezM6xgLhAjO_medium.webp","\/storage\/images\/resized\/PRGhlgB4OKRltSNtT39eA6wlnOTGRap1QQ6FQHih_medium.webp","\/storage\/images\/resized\/s10mcsCV4OAUg9O2KrqOquQC0PhyLMI8hUUkuflM_medium.webp","\/storage\/images\/resized\/eIZgkq1MRZyJ3hBkdupnUUv7wgB6zCl9D99SlPN5_medium.webp","\/storage\/images\/resized\/4QWA67eqfcfyOiA8Wk7YnqroHFqQbTsmDJUYTCTg_medium.webp","\/storage\/images\/resized\/leiAYcRDGTSl5B1eCnwpSGqmDEUEfDPPoYisFGhT_medium.webp","\/storage\/images\/resized\/yNSijlgQghQF53VZuyFLA30CKDe4j3HK74Vtpnxa_medium.webp","\/storage\/images\/resized\/3SpVxcYL33bOvPq4sHxJLH2NeKNeDloahSUpNiO4_medium.webp","\/storage\/images\/resized\/VPE7q24PXoHr5SS2SqfEgxccSMUxWLfZINOX60uo_medium.webp","\/storage\/images\/resized\/mxFdPe9qujsfvfYfcN0QOclAiYORFb0xrRlwV8gs_medium.webp","\/storage\/images\/resized\/hg4jJjT8wVGtHstBCc0zk465Mg9pLx3G4odCDOqE_medium.webp"],"datasets":[{"label":"","data":[49,17,11,10,4,3,3,3,2,2,2,1,1,1,1,1,1,1],"backgroundColor":["#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6","#3B82F6"],"percentage":[39.2,13.6,8.8,8,3.2,2.4,2.4,2.4,1.6,1.6,1.6,0.8,0.8,0.8,0.8,0.8,0.8,0.8],"barThickness":13}]},"options":{"indexAxis":"y","maintainAspectRatio":false,"scales":{"y":{"ticks":{"precision":0,"autoSkip":false,"font":{"family":"Montserrat"},"color":"#000000"}},"x":{"ticks":{"stepSize":null,"precision":0,"font":{"family":"Montserrat"},"color":"#000000"}}},"plugins":{"legend":{"position":"top","labels":{"font":{"family":"Montserrat"},"color":"#000000"}},"title":{"display":true,"text":"Publishers","font":{"size":24,"family":"Montserrat","weight":600},"color":"#000000"}}}}}
Metrics
Cite this
GOST |
RIS |
BibTex |
MLA
Cite this
GOST
Copy
Hafsa N., Arndt D., Wishart D. S. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts // Nucleic Acids Research. 2015. Vol. 43. No. W1. p. W370-W377.
GOST all authors (up to 50)
Copy
Hafsa N., Arndt D., Wishart D. S. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts // Nucleic Acids Research. 2015. Vol. 43. No. W1. p. W370-W377.
Cite this
RIS
Copy
TY - JOUR
DO - 10.1093/nar/gkv494
UR - https://doi.org/10.1093%2Fnar%2Fgkv494
TI - CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts
T2 - Nucleic Acids Research
AU - Hafsa, Noor
AU - Arndt, David
AU - Wishart, David S
PY - 2015
DA - 2015/05/15 00:00:00
PB - Oxford University Press
SP - W370-W377
IS - W1
VL - 43
PMID - 25979265
SN - 0305-1048
SN - 1362-4962
ER -
Cite this
BibTex
Copy
@article{2015_Hafsa,
author = {Noor Hafsa and David Arndt and David S Wishart},
title = {CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts},
journal = {Nucleic Acids Research},
year = {2015},
volume = {43},
publisher = {Oxford University Press},
month = {may},
url = {https://doi.org/10.1093%2Fnar%2Fgkv494},
number = {W1},
pages = {W370--W377},
doi = {10.1093/nar/gkv494}
}
Cite this
MLA
Copy
Hafsa, Noor, et al. “CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.” Nucleic Acids Research, vol. 43, no. W1, May. 2015, pp. W370-W377. https://doi.org/10.1093%2Fnar%2Fgkv494.