Predicted models and CCP4.

CCP4 macromolecular crystallography molecular replacement predicted models structure determination

Journal

Acta crystallographica. Section D, Structural biology
ISSN: 2059-7983
Titre abrégé: Acta Crystallogr D Struct Biol
Pays: United States
ID NLM: 101676043

Informations de publication

Date de publication:
01 Sep 2023
Historique:
received: 12 04 2023
accepted: 19 07 2023
medline: 6 9 2023
pubmed: 18 8 2023
entrez: 18 8 2023
Statut: ppublish

Résumé

In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement.

Identifiants

pubmed: 37594303
pii: S2059798323006289
doi: 10.1107/S2059798323006289
pmc: PMC10478639
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

806-819

Subventions

Organisme : Ministerio de Ciencia e Innovación
ID : PID2021-128751NB-100
Organisme : Ministerio de Ciencia e Innovación
ID : PRE2019-087953

Informations de copyright

open access.

Références

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W526-31
pubmed: 15215442
Proteins. 2021 Dec;89(12):1752-1769
pubmed: 34387010
Acta Crystallogr D Struct Biol. 2022 May 1;78(Pt 5):553-559
pubmed: 35503204
Acta Crystallogr D Struct Biol. 2020 Mar 1;76(Pt 3):209-220
pubmed: 32133986
Acta Crystallogr D Struct Biol. 2022 Dec 1;78(Pt 12):1412-1427
pubmed: 36458613
PLoS One. 2011;6(12):e28766
pubmed: 22163331
Acta Crystallogr D Struct Biol. 2020 Mar 1;76(Pt 3):193-208
pubmed: 32133985
Acta Crystallogr D Biol Crystallogr. 2012 Dec;68(Pt 12):1622-31
pubmed: 23151627
Acta Crystallogr D Struct Biol. 2022 Nov 1;78(Pt 11):1303-1314
pubmed: 36322415
Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):22-5
pubmed: 20057045
Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3637-3641
pubmed: 28325875
Nat Struct Biol. 2003 Dec;10(12):980
pubmed: 14634627
Science. 2023 Mar 17;379(6637):1123-1130
pubmed: 36927031
Nat Commun. 2022 Mar 10;13(1):1265
pubmed: 35273146
Nature. 2021 Aug;596(7873):590-596
pubmed: 34293799
Acta Crystallogr D Struct Biol. 2020 Mar 1;76(Pt 3):248-260
pubmed: 32133989
Acta Crystallogr D Biol Crystallogr. 2007 Apr;63(Pt 4):447-57
pubmed: 17372348
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67
pubmed: 21460454
Nat Biotechnol. 2017 Nov;35(11):1026-1028
pubmed: 29035372
Acta Crystallogr D Struct Biol. 2022 Apr 1;78(Pt 4):517-531
pubmed: 35362474
Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):119-24
pubmed: 18094475
Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2194-201
pubmed: 24189230
Nucleic Acids Res. 2020 Jan 8;48(D1):D570-D578
pubmed: 31696235
Science. 2021 Aug 20;373(6557):871-876
pubmed: 34282049
Nat Rev Mol Cell Biol. 2005 Mar;6(3):197-208
pubmed: 15738986
Nat Methods. 2009 Sep;6(9):651-3
pubmed: 19684596
Nature. 2007 Nov 8;450(7167):259-64
pubmed: 17934447
Nat Methods. 2022 Jun;19(6):679-682
pubmed: 35637307
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8
pubmed: 15980461
Acta Crystallogr D Struct Biol. 2016 Oct 1;72(Pt 10):1149-1161
pubmed: 27710936
Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1955-7
pubmed: 12393928
Proteins. 2022 Nov;90(11):1873-1885
pubmed: 35510704
Nat Methods. 2013 Nov;10(11):1099-101
pubmed: 24037245
Acta Crystallogr D Struct Biol. 2022 Sep 1;78(Pt 9):1079-1089
pubmed: 36048148
Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12180-12185
pubmed: 27663738
Acta Crystallogr D Struct Biol. 2018 Feb 1;74(Pt 2):143-151
pubmed: 29533240
Acta Crystallogr D Struct Biol. 2018 Feb 1;74(Pt 2):68-84
pubmed: 29533233
Cell. 1992 Mar 20;68(6):1145-62
pubmed: 1547508
Nat Protoc. 2008;3(7):1171-9
pubmed: 18600222
Acta Crystallogr D Struct Biol. 2023 Mar 1;79(Pt 3):234-244
pubmed: 36876433
Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2251-6
pubmed: 24189237
Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):205-214
pubmed: 29533228
Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):1-10
pubmed: 18094461
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):183-193
pubmed: 29533226
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):386-94
pubmed: 21460457
Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2266-75
pubmed: 24189239
Bioinformatics. 2017 Jul 15;33(14):2209-2211
pubmed: 28369168
Protein Sci. 2021 Jan;30(1):93-107
pubmed: 32964594
Nucleic Acids Res. 2022 Jan 7;50(D1):D439-D444
pubmed: 34791371
Protein Sci. 2022 Jun;31(6):e4353
pubmed: 35634782
Nat Commun. 2022 Apr 1;13(1):1744
pubmed: 35365655
Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):290-304
pubmed: 29652256
FEBS J. 2014 Sep;281(18):4029-45
pubmed: 24976038
Acta Crystallogr D Biol Crystallogr. 2008 Jan;64(Pt 1):125-32
pubmed: 18094476
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51
pubmed: 16381856
Acta Crystallogr D Struct Biol. 2019 Dec 1;75(Pt 12):1051-1062
pubmed: 31793899
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):328-35
pubmed: 22505253
Acta Crystallogr D Struct Biol. 2022 Jan 1;78(Pt 1):1-13
pubmed: 34981757
Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):338-43
pubmed: 25664744
IUCrJ. 2015 Jan 01;2(Pt 1):95-105
pubmed: 25610631
Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877
pubmed: 31588918
BMC Bioinformatics. 2010 Aug 18;11:431
pubmed: 20718988
Elife. 2022 Mar 03;11:
pubmed: 35238773
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
pubmed: 20124702
Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):245-255
pubmed: 29652252
PLoS Comput Biol. 2022 Aug 22;18(8):e1010483
pubmed: 35994486
Bioinformatics. 2013 Nov 1;29(21):2722-8
pubmed: 23986568
Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2487-99
pubmed: 25195761
Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):167-182
pubmed: 29533225
Acta Crystallogr D Struct Biol. 2018 Feb 1;74(Pt 2):106-116
pubmed: 29533236
Acta Crystallogr D Struct Biol. 2018 Mar 1;74(Pt 3):194-204
pubmed: 29533227
Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11158-62
pubmed: 9736706
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
pubmed: 19461840
Acta Crystallogr D Struct Biol. 2022 Nov 1;78(Pt 11):1283-1293
pubmed: 36322413

Auteurs

Adam J Simpkin (AJ)

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.

Iracema Caballero (I)

Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain.

Stuart McNicholas (S)

York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom.

Kyle Stevenson (K)

UKRI-STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.

Elisabet Jiménez (E)

Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain.

Filomeno Sánchez Rodríguez (F)

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.

Maria Fando (M)

UKRI-STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.

Ville Uski (V)

UKRI-STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.

Charles Ballard (C)

UKRI-STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.

Grzegorz Chojnowski (G)

European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.

Andrey Lebedev (A)

UKRI-STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.

Eugene Krissinel (E)

UKRI-STFC, Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom.

Isabel Usón (I)

Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona, Spain.

Daniel J Rigden (DJ)

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.

Ronan M Keegan (RM)

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.

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