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Items: 1 to 50 of 163

1.

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.

Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD.

Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877. doi: 10.1107/S2059798319011471. Epub 2019 Oct 2.

2.

An oligomeric state-dependent switch in the ER enzyme FICD regulates AMPylation and deAMPylation of BiP.

Perera LA, Rato C, Yan Y, Neidhardt L, McLaughlin SH, Read RJ, Preissler S, Ron D.

EMBO J. 2019 Oct 4;38(21):e102177. doi: 10.15252/embj.2019102177. Epub 2019 Sep 18.

3.

Evaluation of template-based modeling in CASP13.

Croll TI, Sammito MD, Kryshtafovych A, Read RJ.

Proteins. 2019 Aug 13. doi: 10.1002/prot.25800. [Epub ahead of print]

PMID:
31407380
4.

Evaluation of model refinement in CASP13.

Read RJ, Sammito MD, Kryshtafovych A, Croll TI.

Proteins. 2019 Jul 31. doi: 10.1002/prot.25794. [Epub ahead of print]

PMID:
31365160
5.

Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography.

Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN.

J Appl Crystallogr. 2019 Apr 30;52(Pt 3):495-497. doi: 10.1107/S1600576719005922. eCollection 2019 Jun 1.

6.

Germline mutations in the transcription factor IKZF5 cause thrombocytopenia.

Lentaigne C, Greene D, Sivapalaratnam S, Favier R, Seyres D, Thys C, Grassi L, Mangles S, Sibson K, Stubbs MJ, Burden F, Bordet JC, Armari-Alla C, Erber W, Farrow S, Gleadall N, Gomez K, Megy K, Papadia S, Penkett CJ, Sims MC, Stefanucci L, Stephens JC, Read RJ, Stirrups KE, Ouwehand WH, Laffan MA, Frontini M, Freson K, Turro E.

Blood. 2019 Jun 19. pii: blood.2019000782. doi: 10.1182/blood.2019000782. [Epub ahead of print]

PMID:
31217188
7.

Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography.

Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN.

IUCrJ. 2019 Apr 30;6(Pt 3):341-343. doi: 10.1107/S2052252519005918. eCollection 2019 May 1.

8.

Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography.

Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN.

Acta Crystallogr D Struct Biol. 2019 May 1;75(Pt 5):455-457. doi: 10.1107/S2059798319004844. Epub 2019 Apr 29. No abstract available.

9.

Findable Accessible Interoperable Re-usable (FAIR) diffraction data are coming to protein crystallography.

Helliwell JR, Minor W, Weiss MS, Garman EF, Read RJ, Newman J, van Raaij MJ, Hajdu J, Baker EN.

Acta Crystallogr F Struct Biol Commun. 2019 May 1;75(Pt 5):321-323. doi: 10.1107/S2053230X19005909. Epub 2019 Apr 30. No abstract available.

10.

Coping with strong translational noncrystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a.

Jamshidiha M, Pérez-Dorado I, Murray JW, Tate EW, Cota E, Read RJ.

Acta Crystallogr D Struct Biol. 2019 Mar 1;75(Pt 3):342-353. doi: 10.1107/S2059798318017825. Epub 2019 Feb 28.

11.

Structural basis for the specificity of renin-mediated angiotensinogen cleavage.

Yan Y, Zhou A, Carrell RW, Read RJ.

J Biol Chem. 2019 Feb 15;294(7):2353-2364. doi: 10.1074/jbc.RA118.006608. Epub 2018 Dec 18.

12.

Measurement of the total angiotensinogen and its reduced and oxidised forms in human plasma using targeted LC-MS/MS.

Dahabiyeh LA, Tooth D, Carrell RW, Read RJ, Yan Y, Pipkin FB, Barrett DA.

Anal Bioanal Chem. 2019 Jan;411(2):427-437. doi: 10.1007/s00216-018-1455-2. Epub 2018 Nov 21.

13.

Structure and oligomerization of the periplasmic domain of GspL from the type II secretion system of Pseudomonas aeruginosa.

Fulara A, Vandenberghe I, Read RJ, Devreese B, Savvides SN.

Sci Rep. 2018 Nov 13;8(1):16760. doi: 10.1038/s41598-018-34956-w.

14.

Au courant computation of the PDB to audit diffraction anisotropy of soluble and membrane proteins.

Robert X, Kassis-Sahyoun J, Ceres N, Martin J, Sawaya MR, Read RJ, Gouet P, Falson P, Chaptal V.

Data Brief. 2018 May 19;19:753-757. doi: 10.1016/j.dib.2018.05.072. eCollection 2018 Aug.

15.

Real-space refinement in PHENIX for cryo-EM and crystallography.

Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi: 10.1107/S2059798318006551. Epub 2018 May 30.

16.

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination.

Millán C, Sammito MD, McCoy AJ, Nascimento AFZ, Petrillo G, Oeffner RD, Domínguez-Gil T, Hermoso JA, Read RJ, Usón I.

Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):290-304. doi: 10.1107/S2059798318001365. Epub 2018 Apr 3.

17.

Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement.

McCoy AJ, Oeffner RD, Millán C, Sammito M, Usón I, Read RJ.

Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):279-289. doi: 10.1107/S2059798318001353. Epub 2018 Apr 3.

18.

On the application of the expected log-likelihood gain to decision making in molecular replacement.

Oeffner RD, Afonine PV, Millán C, Sammito M, Usón I, Read RJ, McCoy AJ.

Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):245-255. doi: 10.1107/S2059798318004357. Epub 2018 Apr 4.

19.

Maximum-likelihood determination of anomalous substructures.

Read RJ, McCoy AJ.

Acta Crystallogr D Struct Biol. 2018 Feb 1;74(Pt 2):98-105. doi: 10.1107/S2059798317013468. Epub 2018 Feb 1.

20.

X-ray diffraction reveals the intrinsic difference in the physical properties of membrane and soluble proteins.

Robert X, Kassis-Sahyoun J, Ceres N, Martin J, Sawaya MR, Read RJ, Gouet P, Falson P, Chaptal V.

Sci Rep. 2017 Dec 5;7(1):17013. doi: 10.1038/s41598-017-17216-1.

21.

AMPylation targets the rate-limiting step of BiP's ATPase cycle for its functional inactivation.

Preissler S, Rohland L, Yan Y, Chen R, Read RJ, Ron D.

Elife. 2017 Oct 24;6. pii: e29428. doi: 10.7554/eLife.29428.

22.

Insights into Hunter syndrome from the structure of iduronate-2-sulfatase.

Demydchuk M, Hill CH, Zhou A, Bunkóczi G, Stein PE, Marchesan D, Deane JE, Read RJ.

Nat Commun. 2017 Jun 8;8:15786. doi: 10.1038/ncomms15786.

23.

Responses to `Atomic resolution': a badly abused term in structural biology.

Chiu W, Holton J, Langan P, Sauter NK, Schlichting I, Terwilliger T, Martin JL, Read RJ, Wakatsuki S.

Acta Crystallogr D Struct Biol. 2017 Apr 1;73(Pt 4):381-383. doi: 10.1107/S205979831700417X. Epub 2017 Mar 31. No abstract available.

PMID:
28375150
24.

Ab initio solution of macromolecular crystal structures without direct methods.

McCoy AJ, Oeffner RD, Wrobel AG, Ojala JR, Tryggvason K, Lohkamp B, Read RJ.

Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):3637-3641. doi: 10.1073/pnas.1701640114. Epub 2017 Mar 21.

25.

Decoding Corticotropin-Releasing Factor Receptor Type 1 Crystal Structures.

Dore AS, Bortolato A, Hollenstein K, Cheng RKY, Read RJ, Marshall FH.

Curr Mol Pharmacol. 2017;10(4):334-344. doi: 10.2174/1874467210666170110114727.

26.

How serpins transport hormones and regulate their release.

Carrell RW, Read RJ.

Semin Cell Dev Biol. 2017 Feb;62:133-141. doi: 10.1016/j.semcdb.2016.12.007. Epub 2016 Dec 24. Review.

PMID:
28027946
27.

Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.

Felix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN.

Nat Commun. 2016 Nov 7;7:13228. doi: 10.1038/ncomms13228.

28.

A critical examination of the recently reported crystal structures of the human SMN protein.

Weiss MS, Diederichs K, Read RJ, Panjikar S, Van Duyne GD, Matera AG, Fischer U, Grimm C.

Hum Mol Genet. 2016 Aug 29;25(21):4717–4725. doi: 10.1093/hmg/ddw298.

29.

Structure of Gremlin-2 in Complex with GDF5 Gives Insight into DAN-Family-Mediated BMP Antagonism.

Nolan K, Kattamuri C, Rankin SA, Read RJ, Zorn AM, Thompson TB.

Cell Rep. 2016 Aug 23;16(8):2077-2086. doi: 10.1016/j.celrep.2016.07.046. Epub 2016 Aug 11.

30.

Molecular Mechanism of Z α1-Antitrypsin Deficiency.

Huang X, Zheng Y, Zhang F, Wei Z, Wang Y, Carrell RW, Read RJ, Chen GQ, Zhou A.

J Biol Chem. 2016 Jul 22;291(30):15674-86. doi: 10.1074/jbc.M116.727826. Epub 2016 May 31.

31.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J.

Structure. 2016 Apr 5;24(4):502-508. doi: 10.1016/j.str.2016.02.017.

32.

A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error.

Read RJ, McCoy AJ.

Acta Crystallogr D Struct Biol. 2016 Mar;72(Pt 3):375-87. doi: 10.1107/S2059798315013236. Epub 2016 Mar 1.

33.

Expanding beyond biological crystallography.

Martin JL, Read RJ, Wakatsuki S.

Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):1. doi: 10.1107/S2059798315023761. Epub 2016 Jan 1. No abstract available.

PMID:
26894528
34.

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement.

Jackson RN, McCoy AJ, Terwilliger TC, Read RJ, Wiedenheft B.

Nat Protoc. 2015 Sep;10(9):1275-84. doi: 10.1038/nprot.2015.069. Epub 2015 Jul 30.

35.

Structure of human saposin A at lysosomal pH.

Hill CH, Read RJ, Deane JE.

Acta Crystallogr F Struct Biol Commun. 2015 Jul;71(Pt 7):895-900. doi: 10.1107/S2053230X15008584. Epub 2015 Jun 27.

36.

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.

Structure. 2015 Jul 7;23(7):1156-67. doi: 10.1016/j.str.2015.05.013. Epub 2015 Jun 18.

37.

Azasugar inhibitors as pharmacological chaperones for Krabbe disease.

Hill CH, Viuff AH, Spratley SJ, Salamone S, Christensen SH, Read RJ, Moriarty NW, Jensen HH, Deane JE.

Chem Sci. 2015 May 20;6(5):3075-3086. Epub 2015 Mar 30.

38.

ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning.

Sliwiak J, Dauter Z, Kowiel M, McCoy AJ, Read RJ, Jaskolski M.

Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):829-43. doi: 10.1107/S1399004715001388. Epub 2015 Mar 26.

39.

G-actin provides substrate-specificity to eukaryotic initiation factor 2α holophosphatases.

Chen R, Rato C, Yan Y, Crespillo-Casado A, Clarke HJ, Harding HP, Marciniak SJ, Read RJ, Ron D.

Elife. 2015 Mar 16;4. doi: 10.7554/eLife.04871.

40.

Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement.

Bunkóczi G, Wallner B, Read RJ.

Structure. 2015 Feb 3;23(2):397-406. doi: 10.1016/j.str.2014.11.020. Epub 2015 Jan 22.

41.

Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.

Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC.

Nat Methods. 2015 Feb;12(2):127-30. doi: 10.1038/nmeth.3212. Epub 2014 Dec 22.

42.

Towards engineering hormone-binding globulins as drug delivery agents.

Chan WL, Zhou A, Read RJ.

PLoS One. 2014 Nov 26;9(11):e113402. doi: 10.1371/journal.pone.0113402. eCollection 2014.

43.

Transcriptional diversity during lineage commitment of human blood progenitors.

Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SBG, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium B, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HHD, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A.

Science. 2014 Sep 26;345(6204):1251033. doi: 10.1126/science.1251033.

44.

Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli.

Jackson RN, Golden SM, van Erp PB, Carter J, Westra ER, Brouns SJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B.

Science. 2014 Sep 19;345(6203):1473-9. doi: 10.1126/science.1256328. Epub 2014 Aug 7.

45.

Automated identification of elemental ions in macromolecular crystal structures.

Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Apr;70(Pt 4):1104-14. doi: 10.1107/S1399004714001308. Epub 2014 Mar 20.

46.

Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry.

Sliwiak J, Jaskolski M, Dauter Z, McCoy AJ, Read RJ.

Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):471-80. doi: 10.1107/S1399004713030319. Epub 2014 Jan 29.

47.

Temperature-responsive release of thyroxine and its environmental adaptation in Australians.

Qi X, Chan WL, Read RJ, Zhou A, Carrell RW.

Proc Biol Sci. 2014 Jan 29;281(1779):20132747. doi: 10.1098/rspb.2013.2747. Print 2014 Mar 22.

48.

Automating crystallographic structure solution and refinement of protein-ligand complexes.

Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):144-54. doi: 10.1107/S139900471302748X. Epub 2013 Dec 25.

49.

Structural snapshots illustrate the catalytic cycle of β-galactocerebrosidase, the defective enzyme in Krabbe disease.

Hill CH, Graham SC, Read RJ, Deane JE.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20479-84. doi: 10.1073/pnas.1311990110. Epub 2013 Dec 2.

50.

Phaser.MRage: automated molecular replacement.

Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2276-86. doi: 10.1107/S0907444913022750. Epub 2013 Oct 18. Review.

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