Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver.
AlphaFold2
collision cross section
ion mobility
mass spectrometry
protein structure prediction
webserver
Journal
Briefings in bioinformatics
ISSN: 1477-4054
Titre abrégé: Brief Bioinform
Pays: England
ID NLM: 100912837
Informations de publication
Date de publication:
20 09 2023
20 09 2023
Historique:
received:
20
04
2023
revised:
03
07
2023
accepted:
08
08
2023
pmc-release:
22
08
2024
medline:
25
9
2023
pubmed:
23
8
2023
entrez:
23
8
2023
Statut:
ppublish
Résumé
Ion mobility coupled to mass spectrometry informs on the shape and size of protein structures in the form of a collision cross section (CCSIM). Although there are several computational methods for predicting CCSIM based on protein structures, including our previously developed projection approximation using rough circular shapes (PARCS), the process usually requires prior experience with the command-line interface. To overcome this challenge, here we present a web application on the Rosetta Online Server that Includes Everyone (ROSIE) webserver to predict CCSIM from protein structure using projection approximation with PARCS. In this web interface, the user is only required to provide one or more PDB files as input. Results from our case studies suggest that CCSIM predictions (with ROSIE-PARCS) are highly accurate with an average error of 6.12%. Furthermore, the absolute difference between CCSIM and CCSPARCS can help in distinguishing accurate from inaccurate AlphaFold2 protein structure predictions. ROSIE-PARCS is designed with a user-friendly interface, is available publicly and is free to use. The ROSIE-PARCS web interface is supported by all major web browsers and can be accessed via this link (https://rosie.graylab.jhu.edu).
Identifiants
pubmed: 37609950
pii: 7247509
doi: 10.1093/bib/bbad308
pmc: PMC10516336
pii:
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIGMS NIH HHS
ID : P41 GM128577
Pays : United States
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Références
J Am Soc Mass Spectrom. 2019 Jan;30(1):113-117
pubmed: 29736599
Analyst. 2011 Jan 7;136(1):20-8
pubmed: 20820495
Anal Chem. 2020 Sep 15;92(18):12297-12303
pubmed: 32660238
J Chem Theory Comput. 2021 Apr 13;17(4):2619-2629
pubmed: 33780620
Chem Rev. 2020 Apr 8;120(7):3328-3380
pubmed: 31851501
J Phys Chem B. 2011 Oct 27;115(42):12266-75
pubmed: 21905704
Proteins. 2009;77 Suppl 9:89-99
pubmed: 19701941
Nat Methods. 2022 Nov;19(11):1376-1382
pubmed: 36266465
Anal Chem. 2020 Mar 17;92(6):4475-4483
pubmed: 32048834
Curr Opin Chem Biol. 2018 Feb;42:93-100
pubmed: 29207278
Structure. 2018 Apr 3;26(4):599-606.e3
pubmed: 29576318
Anal Chem. 2022 Jul 26;94(29):10506-10514
pubmed: 35834801
Protein Sci. 2018 Jan;27(1):245-258
pubmed: 28960548
Annu Rev Biochem. 2008;77:443-77
pubmed: 18318657
Biochemistry. 2017 Dec 5;56(48):6329-6342
pubmed: 29099587
J Phys Chem B. 2022 Oct 27;126(42):8439-8446
pubmed: 36251522
J Chem Phys. 2020 Dec 28;153(24):240901
pubmed: 33380110
Protein Sci. 2001 Jul;10(7):1470-3
pubmed: 11420449
Anal Chem. 2019 Dec 17;91(24):15709-15717
pubmed: 31710208
Annu Rev Phys Chem. 2022 Apr 20;73:1-19
pubmed: 34724394
Anal Chem. 2021 Jun 1;93(21):7596-7605
pubmed: 33999617
J Chem Inf Model. 2020 May 26;60(5):2522-2532
pubmed: 31872764
Methods Enzymol. 2011;487:545-74
pubmed: 21187238
PLoS One. 2013 May 22;8(5):e63906
pubmed: 23717507
Structure. 2022 Feb 3;30(2):313-320.e3
pubmed: 34739840
ACS Cent Sci. 2019 Aug 28;5(8):1330-1341
pubmed: 31482115
Sci Rep. 2017 Jul 3;7(1):4552
pubmed: 28674401
J Phys Chem B. 2019 Aug 22;123(33):7103-7112
pubmed: 31411026
Acc Chem Res. 2014 Apr 15;47(4):1010-8
pubmed: 24524650
Elife. 2022 Nov 08;11:
pubmed: 36346217
J Am Soc Mass Spectrom. 2019 May;30(5):876-885
pubmed: 30887458
Nat Commun. 2022 Jul 28;13(1):4377
pubmed: 35902583
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Nat Commun. 2022 Dec 21;13(1):7846
pubmed: 36543826
Protein Sci. 2021 Jan;30(1):250-261
pubmed: 33166013
Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8143-8148
pubmed: 30944216
J Am Soc Mass Spectrom. 2022 Mar 2;33(3):584-591
pubmed: 35147431
J Am Soc Mass Spectrom. 2017 Oct;28(10):1991-2000
pubmed: 28752478
Anal Chim Acta. 2014 Jan 15;808:44-55
pubmed: 24370092
J Chem Theory Comput. 2019 May 14;15(5):3410-3424
pubmed: 30946594
Nat Commun. 2019 Jan 14;10(1):192
pubmed: 30643114
Curr Opin Chem Biol. 2006 Oct;10(5):402-8
pubmed: 16935553
Acta Crystallogr D Biol Crystallogr. 2002 Jun;58(Pt 6 No 1):899-907
pubmed: 12037327
J Am Soc Mass Spectrom. 2017 Jan;28(1):5-13
pubmed: 27909974
Methods Mol Biol. 2020;2084:1-31
pubmed: 31729651
J Mol Biol. 2013 Nov 29;425(23):4790-801
pubmed: 23583780
J Phys Chem B. 2017 Apr 20;121(15):3493-3501
pubmed: 27807976
Structure. 2012 Sep 5;20(9):1596-609
pubmed: 22841294
Mol Cell Proteomics. 2016 Jul;15(7):2491-500
pubmed: 27150526
Anal Chem. 2021 Jun 15;93(23):8188-8195
pubmed: 34061512
Analyst. 2015 Oct 21;140(20):6804-13
pubmed: 26178623
Nat Commun. 2021 Jan 12;12(1):341
pubmed: 33436604
Analyst. 2016 Feb 7;141(3):884-91
pubmed: 26739109
Curr Opin Chem Biol. 2018 Feb;42:51-59
pubmed: 29154177
J Am Soc Mass Spectrom. 2017 Apr;28(4):587-596
pubmed: 28194738
PLoS One. 2013 Sep 17;8(9):e73411
pubmed: 24069194
Nat Methods. 2020 Jul;17(7):665-680
pubmed: 32483333
Structure. 2015 Apr 7;23(4):791-9
pubmed: 25800554
Anal Chem. 2018 Jun 19;90(12):7721-7729
pubmed: 29874044
J Phys Chem B. 2019 Apr 4;123(13):2756-2769
pubmed: 30866623
J Phys Chem B. 2018 Apr 12;122(14):3920-3930
pubmed: 29595057
Methods. 2015 Nov 1;89:13-21
pubmed: 25782628
Mass Spectrom Rev. 2009 Sep-Oct;28(5):785-815
pubmed: 19016300
Protein Sci. 2019 Jun;28(6):1024-1030
pubmed: 30927297
Nat Protoc. 2008;3(7):1139-52
pubmed: 18600219
Structure. 2019 Nov 5;27(11):1716-1720.e1
pubmed: 31519398
J Chem Theory Comput. 2017 Oct 10;13(10):5131-5145
pubmed: 28949136