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Items: 1 to 50 of 94

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.

Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation.

Wrobel AG, Kadlecova Z, Kamenicky J, Yang JC, Herrmann T, Kelly BT, McCoy AJ, Evans PR, Martin S, Müller S, Sroubek F, Neuhaus D, Höning S, Owen DJ.

Dev Cell. 2019 Aug 19;50(4):494-508.e11. doi: 10.1016/j.devcel.2019.07.017.

3.

Distribution of Capsular Types of Campylobacter jejuni Isolates from Symptomatic and Asymptomatic Children in Peru.

Rojas JD, Reynolds ND, Pike BL, Espinoza NM, Kuroiwa J, Jani V, Ríos PA, Nunez RG, Yori PP, Bernal M, Meza RA, Kosek MN, McCoy AJ, Simons MP, Gregory MJ, Guerry P, Poly FM.

Am J Trop Med Hyg. 2019 Sep;101(3):541-548. doi: 10.4269/ajtmh.18-0994.

4.

Erratum for Ramakrishnan et al., "Enhanced Immunogenicity and Protective Efficacy of a Campylobacter jejuni Conjugate Vaccine Coadministered with Liposomes Containing Monophosphoryl Lipid A and QS-21".

Ramakrishnan A, Schumack NM, Gariepy CL, Eggleston H, Nunez G, Espinoza N, Nieto M, Castillo R, Rojas J, McCoy AJ, Beck Z, Matyas GR, Alving CR, Guerry P, Poly F, Laird RM.

mSphere. 2019 Jun 26;4(3). pii: e00440-19. doi: 10.1128/mSphere.00440-19. No abstract available.

5.

Correction for Ramakrishnan et al., "Enhanced Immunogenicity and Protective Efficacy of a Campylobacter jejuni Conjugate Vaccine Coadministered with Liposomes Containing Monophosphoryl Lipid A and QS-21".

Ramakrishnan A, Schumack NM, Gariepy CL, Eggleston H, Nunez G, Espinoza N, Nieto M, Castillo R, Rojas J, McCoy AJ, Beck Z, Matyas GR, Alving CR, Guerry P, Poly F, Laird RM.

mSphere. 2019 May 22;4(3). pii: e00351-19. doi: 10.1128/mSphere.00351-19. No abstract available.

6.

Enhanced Immunogenicity and Protective Efficacy of a Campylobacter jejuni Conjugate Vaccine Coadministered with Liposomes Containing Monophosphoryl Lipid A and QS-21.

Ramakrishnan A, Schumack NM, Gariepy CL, Eggleston H, Nunez G, Espinoza N, Nieto M, Castillo R, Rojas J, McCoy AJ, Beck Z, Matyas GR, Alving CR, Guerry P, Poly F, Laird RM.

mSphere. 2019 May 1;4(3). pii: e00101-19. doi: 10.1128/mSphere.00101-19. Erratum in: mSphere. 2019 May 22;4(3):. mSphere. 2019 Jun 26;4(3):.

7.

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.

8.

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.

9.

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.

10.

Campylobacter jejuni transcriptional and genetic adaptation during human infection.

Crofts AA, Poly FM, Ewing CP, Kuroiwa JM, Rimmer JE, Harro C, Sack D, Talaat KR, Porter CK, Gutierrez RL, DeNearing B, Brubaker J, Laird RM, Maue AC, Jaep K, Alcala A, Tribble DR, Riddle MS, Ramakrishnan A, McCoy AJ, Davies BW, Guerry P, Trent MS.

Nat Microbiol. 2018 Apr;3(4):494-502. doi: 10.1038/s41564-018-0133-7. Epub 2018 Mar 27.

11.

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.

12.

Neuronal correlates of ketamine and walking induced gamma oscillations in the medial prefrontal cortex and mediodorsal thalamus.

Furth KE, McCoy AJ, Dodge C, Walters JR, Buonanno A, Delaville C.

PLoS One. 2017 Nov 2;12(11):e0186732. doi: 10.1371/journal.pone.0186732. eCollection 2017.

13.

Structure and evolution of ENTH and VHS/ENTH-like domains in tepsin.

Archuleta TL, Frazier MN, Monken AE, Kendall AK, Harp J, McCoy AJ, Creanza N, Jackson LP.

Traffic. 2017 Sep;18(9):590-603. doi: 10.1111/tra.12499.

14.

Acknowledging Errors: Advanced Molecular Replacement with Phaser.

McCoy AJ.

Methods Mol Biol. 2017;1607:421-453. doi: 10.1007/978-1-4939-7000-1_18. Review.

PMID:
28573584
15.

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.

16.

Transient Fcho1/2⋅Eps15/R⋅AP-2 Nanoclusters Prime the AP-2 Clathrin Adaptor for Cargo Binding.

Ma L, Umasankar PK, Wrobel AG, Lymar A, McCoy AJ, Holkar SS, Jha A, Pradhan-Sundd T, Watkins SC, Owen DJ, Traub LM.

Dev Cell. 2016 Jun 6;37(5):428-43. doi: 10.1016/j.devcel.2016.05.003. Epub 2016 May 26.

17.

Ventral Medial Thalamic Nucleus Promotes Synchronization of Increased High Beta Oscillatory Activity in the Basal Ganglia-Thalamocortical Network of the Hemiparkinsonian Rat.

Brazhnik E, McCoy AJ, Novikov N, Hatch CE, Walters JR.

J Neurosci. 2016 Apr 13;36(15):4196-208. doi: 10.1523/JNEUROSCI.3582-15.2016.

18.

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.

19.

Advances in experimental phasing.

McCoy AJ, Schneider T.

Acta Crystallogr D Struct Biol. 2016 Mar;72(Pt 3):291-2. doi: 10.1107/S2059798316003375. Epub 2016 Mar 1. No abstract available.

20.

Effects of L-dopa priming on cortical high beta and high gamma oscillatory activity in a rodent model of Parkinson's disease.

Dupre KB, Cruz AV, McCoy AJ, Delaville C, Gerber CM, Eyring KW, Walters JR.

Neurobiol Dis. 2016 Feb;86:1-15. doi: 10.1016/j.nbd.2015.11.009. Epub 2015 Nov 14.

21.

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.

22.

Subthalamic nucleus activity in the awake hemiparkinsonian rat: relationships with motor and cognitive networks.

Delaville C, McCoy AJ, Gerber CM, Cruz AV, Walters JR.

J Neurosci. 2015 Apr 29;35(17):6918-30. doi: 10.1523/JNEUROSCI.0587-15.2015.

23.

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.

24.

Oscillatory Activity in Basal Ganglia and Motor Cortex in an Awake Behaving Rodent Model of Parkinson's Disease.

Delaville C, Cruz AV, McCoy AJ, Brazhnik E, Avila I, Novikov N, Walters JR.

Basal Ganglia. 2014 Apr 1;3(4):221-227.

25.

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.

26.

A toolbox for spatiotemporal analysis of voltage-sensitive dye imaging data in brain slices.

Bourgeois EB, Johnson BN, McCoy AJ, Trippa L, Cohen AS, Marsh ED.

PLoS One. 2014 Sep 26;9(9):e108686. doi: 10.1371/journal.pone.0108686. eCollection 2014.

27.

Functional correlates of exaggerated oscillatory activity in basal ganglia output in hemiparkinsonian rats.

Brazhnik E, Novikov N, McCoy AJ, Cruz AV, Walters JR.

Exp Neurol. 2014 Nov;261:563-77. doi: 10.1016/j.expneurol.2014.07.010. Epub 2014 Jul 30.

28.

Promiscuous and adaptable enzymes fill "holes" in the tetrahydrofolate pathway in Chlamydia species.

Adams NE, Thiaville JJ, Proestos J, Juárez-Vázquez AL, McCoy AJ, Barona-Gómez F, Iwata-Reuyl D, de Crécy-Lagard V, Maurelli AT.

MBio. 2014 Jul 8;5(4):e01378-14. doi: 10.1128/mBio.01378-14.

29.

VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface.

Hesketh GG, Pérez-Dorado I, Jackson LP, Wartosch L, Schäfer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MNJ, Luzio JP, Owen DJ.

Dev Cell. 2014 Jun 9;29(5):591-606. doi: 10.1016/j.devcel.2014.04.010. Epub 2014 May 22.

30.

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.

31.

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.

32.

Structures of yeast mitochondrial ADP/ATP carriers support a domain-based alternating-access transport mechanism.

Ruprecht JJ, Hellawell AM, Harding M, Crichton PG, McCoy AJ, Kunji ER.

Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):E426-34. doi: 10.1073/pnas.1320692111. Epub 2014 Jan 13.

33.

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.

34.

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.

35.

SCEDS: protein fragments for molecular replacement in Phaser.

McCoy AJ, Nicholls RA, Schneider TR.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2216-25. doi: 10.1107/S0907444913021811. Epub 2013 Oct 4.

36.

Improved estimates of coordinate error for molecular replacement.

Oeffner RD, Bunkóczi G, McCoy AJ, Read RJ.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2209-15. doi: 10.1107/S0907444913023512. Epub 2013 Oct 12.

37.

DNA prime/Adenovirus boost malaria vaccine encoding P. falciparum CSP and AMA1 induces sterile protection associated with cell-mediated immunity.

Chuang I, Sedegah M, Cicatelli S, Spring M, Polhemus M, Tamminga C, Patterson N, Guerrero M, Bennett JW, McGrath S, Ganeshan H, Belmonte M, Farooq F, Abot E, Banania JG, Huang J, Newcomer R, Rein L, Litilit D, Richie NO, Wood C, Murphy J, Sauerwein R, Hermsen CC, McCoy AJ, Kamau E, Cummings J, Komisar J, Sutamihardja A, Shi M, Epstein JE, Maiolatesi S, Tosh D, Limbach K, Angov E, Bergmann-Leitner E, Bruder JT, Doolan DL, King CR, Carucci D, Dutta S, Soisson L, Diggs C, Hollingdale MR, Ockenhouse CF, Richie TL.

PLoS One. 2013;8(2):e55571. doi: 10.1371/journal.pone.0055571. Epub 2013 Feb 14.

38.

Intensity statistics in the presence of translational noncrystallographic symmetry.

Read RJ, Adams PD, McCoy AJ.

Acta Crystallogr D Biol Crystallogr. 2013 Feb;69(Pt 2):176-83. doi: 10.1107/S0907444912045374. Epub 2013 Jan 16.

39.

Intercondylar synovial septum in two patients with nail-patella syndrome.

Heckman DS, McCoy AJ, Spritzer CE, Garrett WE.

J Knee Surg. 2013 Dec;26 Suppl 1:S107-11. doi: 10.1055/s-0032-1324809. Epub 2012 Sep 21.

PMID:
23288746
40.

Twenty years of work-related injury and illness among union carpenters in Washington State.

McCoy AJ, Kucera KL, Schoenfisch AL, Silverstein BA, Lipscomb HJ.

Am J Ind Med. 2013 Apr;56(4):381-8. doi: 10.1002/ajim.22134. Epub 2012 Nov 9.

PMID:
23143816
41.

Graphical tools for macromolecular crystallography in PHENIX.

Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD.

J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.

42.

State-dependent spike and local field synchronization between motor cortex and substantia nigra in hemiparkinsonian rats.

Brazhnik E, Cruz AV, Avila I, Wahba MI, Novikov N, Ilieva NM, McCoy AJ, Gerber C, Walters JR.

J Neurosci. 2012 Jun 6;32(23):7869-80. doi: 10.1523/JNEUROSCI.0943-12.2012.

43.

The Phenix software for automated determination of macromolecular structures.

Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH.

Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.

44.

Using SAD data in Phaser.

Read RJ, McCoy AJ.

Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-44. doi: 10.1107/S0907444910051371. Epub 2011 Mar 5.

45.

Differential regulation of caspase-1 activation via NLRP3/NLRC4 inflammasomes mediated by aerolysin and type III secretion system during Aeromonas veronii infection.

McCoy AJ, Koizumi Y, Higa N, Suzuki T.

J Immunol. 2010 Dec 1;185(11):7077-84. doi: 10.4049/jimmunol.1002165. Epub 2010 Oct 29.

46.

Restoration of PPARγ reverses lipid accumulation in alveolar macrophages of GM-CSF knockout mice.

Malur A, Baker AD, McCoy AJ, Wells G, Barna BP, Kavuru MS, Malur AG, Thomassen MJ.

Am J Physiol Lung Cell Mol Physiol. 2011 Jan;300(1):L73-80. doi: 10.1152/ajplung.00128.2010. Epub 2010 Oct 29.

47.

Cytotoxins of the human pathogen Aeromonas hydrophila trigger, via the NLRP3 inflammasome, caspase-1 activation in macrophages.

McCoy AJ, Koizumi Y, Toma C, Higa N, Dixit V, Taniguchi S, Tschopp J, Suzuki T.

Eur J Immunol. 2010 Oct;40(10):2797-803. doi: 10.1002/eji.201040490.

48.

A large-scale conformational change couples membrane recruitment to cargo binding in the AP2 clathrin adaptor complex.

Jackson LP, Kelly BT, McCoy AJ, Gaffry T, James LC, Collins BM, Höning S, Evans PR, Owen DJ.

Cell. 2010 Jun 25;141(7):1220-9. doi: 10.1016/j.cell.2010.05.006.

49.

Experimental phasing: best practice and pitfalls.

McCoy AJ, Read RJ.

Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):458-69. doi: 10.1107/S0907444910006335. Epub 2010 Mar 24.

50.

Pathogenic Vibrio activate NLRP3 inflammasome via cytotoxins and TLR/nucleotide-binding oligomerization domain-mediated NF-kappa B signaling.

Toma C, Higa N, Koizumi Y, Nakasone N, Ogura Y, McCoy AJ, Franchi L, Uematsu S, Sagara J, Taniguchi S, Tsutsui H, Akira S, Tschopp J, Núñez G, Suzuki T.

J Immunol. 2010 May 1;184(9):5287-97. doi: 10.4049/jimmunol.0903536. Epub 2010 Mar 26.

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