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Items: 31

1.

Cryo-EM map interpretation and protein model-building using iterative map segmentation.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

Protein Sci. 2019 Oct 9. doi: 10.1002/pro.3740. [Epub ahead of print]

PMID:
31599033
2.

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.

PMID:
31588918
3.

Extracorporeal photochemotherapy induces bona fide immunogenic cell death.

Tatsuno K, Yamazaki T, Hanlon D, Han P, Robinson E, Sobolev O, Yurter A, Rivera-Molina F, Arshad N, Edelson RL, Galluzzi L.

Cell Death Dis. 2019 Aug 2;10(8):578. doi: 10.1038/s41419-019-1819-3.

4.

Cryo_fit: Democratization of flexible fitting for cryo-EM.

Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K.

J Struct Biol. 2019 Oct 1;208(1):1-6. doi: 10.1016/j.jsb.2019.05.012. Epub 2019 Jul 3.

PMID:
31279069
5.

Novel Protocol for Generating Physiologic Immunogenic Dendritic Cells.

Ventura A, Vassall A, Yurter A, Robinson E, Filler R, Hanlon D, Meeth K, Ezaldein H, Girardi M, Sobolev O, Bosenberg MW, Edelson RL.

J Vis Exp. 2019 May 17;(147). doi: 10.3791/59370.

PMID:
31157760
6.

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY.

Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):451-454. doi: 10.1107/S2059798319004522. Epub 2019 Apr 8. No abstract available.

PMID:
30988261
7.

Magnetoelastic hybrid excitations in CeAuAl3.

Čermák P, Schneidewind A, Liu B, Koza MM, Franz C, Schönmann R, Sobolev O, Pfleiderer C.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6695-6700. doi: 10.1073/pnas.1819664116. Epub 2019 Mar 20.

8.

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

Nat Methods. 2018 Nov;15(11):905-908. doi: 10.1038/s41592-018-0173-1. Epub 2018 Oct 30.

9.

New tools for the analysis and validation of cryo-EM maps and atomic models.

Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A.

Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):814-840. doi: 10.1107/S2059798318009324. Epub 2018 Sep 3.

10.

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

J Struct Biol. 2018 Nov;204(2):338-343. doi: 10.1016/j.jsb.2018.07.016. Epub 2018 Jul 29.

11.

Automated map sharpening by maximization of detail and connectivity.

Terwilliger TC, Sobolev OV, Afonine PV, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):545-559. doi: 10.1107/S2059798318004655. Epub 2018 May 18.

12.

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.

13.

Extracorporeal Photochemotherapy Drives Monocyte-to-Dendritic Cell Maturation to Induce Anticancer Immunity.

Ventura A, Vassall A, Robinson E, Filler R, Hanlon D, Meeth K, Ezaldein H, Girardi M, Sobolev O, Bosenberg MW, Edelson RL.

Cancer Res. 2018 Jul 15;78(14):4045-4058. doi: 10.1158/0008-5472.CAN-18-0171. Epub 2018 May 15.

14.

Antiferromagnetic correlations in the metallic strongly correlated transition metal oxide LaNiO3.

Guo H, Li ZW, Zhao L, Hu Z, Chang CF, Kuo CY, Schmidt W, Piovano A, Pi TW, Sobolev O, Khomskii DI, Tjeng LH, Komarek AC.

Nat Commun. 2018 Jan 3;9(1):43. doi: 10.1038/s41467-017-02524-x.

15.

Polder maps: improving OMIT maps by excluding bulk solvent.

Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD.

Acta Crystallogr D Struct Biol. 2017 Feb 1;73(Pt 2):148-157. doi: 10.1107/S2059798316018210. Epub 2017 Feb 1.

16.

De Gennes Narrowing and Hard-Sphere Approach.

Sobolev O.

J Phys Chem B. 2016 Sep 22;120(37):9969-77. doi: 10.1021/acs.jpcb.6b04685. Epub 2016 Sep 13.

PMID:
27583769
17.

Induction of anti-tumor CD8 T cell responses by experimental ECP-induced human dendritic antigen presenting cells.

Kibbi N, Sobolev O, Girardi M, Edelson RL.

Transfus Apher Sci. 2016 Aug;55(1):146-52. doi: 10.1016/j.transci.2016.06.001. Epub 2016 Jun 6.

PMID:
27317354
18.

Incommensurate spin correlations in highly oxidized cobaltates La2-xSrxCoO4.

Li ZW, Drees Y, Kuo CY, Guo H, Ricci A, Lamago D, Sobolev O, Rütt U, Gutowski O, Pi TW, Piovano A, Schmidt W, Mogare K, Hu Z, Tjeng LH, Komarek AC.

Sci Rep. 2016 Apr 27;6:25117. doi: 10.1038/srep25117.

19.

Corrigendum: Adjuvanted influenza-H1N1 vaccination reveals lymphoid signatures of age-dependent early responses and of clinical adverse events.

Sobolev O, Binda E, O'Farrell S, Lorenc A, Pradines J, Huang Y, Duffner J, Schulz R, Cason J, Zambon M, Malim MH, Peakman M, Cope A, Capila I, Kaundinya GV, Hayday AC.

Nat Immunol. 2016 Apr;17(4):469. doi: 10.1038/ni0416-469b. No abstract available.

PMID:
27002849
20.

Adjuvanted influenza-H1N1 vaccination reveals lymphoid signatures of age-dependent early responses and of clinical adverse events.

Sobolev O, Binda E, O'Farrell S, Lorenc A, Pradines J, Huang Y, Duffner J, Schulz R, Cason J, Zambon M, Malim MH, Peakman M, Cope A, Capila I, Kaundinya GV, Hayday AC.

Nat Immunol. 2016 Feb;17(2):204-13. doi: 10.1038/ni.3328. Epub 2016 Jan 4. Erratum in: Nat Immunol. 2016 Apr;17(4):469.

21.

Programming new geometry restraints: parallelity of atomic groups.

Sobolev OV, Afonine PV, Adams PD, Urzhumtsev A.

J Appl Crystallogr. 2015 Jul 8;48(Pt 4):1130-1141. eCollection 2015 Aug 1.

22.

FEM: feature-enhanced map.

Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2015 Mar;71(Pt 3):646-66. doi: 10.1107/S1399004714028132. Epub 2015 Feb 26.

23.

Hour-glass magnetic excitations induced by nanoscopic phase separation in cobalt oxides.

Drees Y, Li ZW, Ricci A, Rotter M, Schmidt W, Lamago D, Sobolev O, Rütt U, Gutowski O, Sprung M, Piovano A, Castellan JP, Komarek AC.

Nat Commun. 2014 Dec 23;5:5731. doi: 10.1038/ncomms6731.

PMID:
25534540
24.

Immunological visibility: posttranscriptional regulation of human NKG2D ligands by the EGF receptor pathway.

Vantourout P, Willcox C, Turner A, Swanson CM, Haque Y, Sobolev O, Grigoriadis A, Tutt A, Hayday A.

Sci Transl Med. 2014 Apr 9;6(231):231ra49. doi: 10.1126/scitranslmed.3007579.

25.

Detection of alternative conformations by unrestrained refinement.

Sobolev OV, Lunin VY.

Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1118-27. doi: 10.1107/S0907444912021269. Epub 2012 Aug 18.

PMID:
22948912
26.

The intraepithelial T cell response to NKG2D-ligands links lymphoid stress surveillance to atopy.

Strid J, Sobolev O, Zafirova B, Polic B, Hayday A.

Science. 2011 Dec 2;334(6060):1293-7. doi: 10.1126/science.1211250.

27.

Natural killer cells require selectins for suppression of subcutaneous tumors.

Sobolev O, Stern P, Lacy-Hulbert A, Hynes RO.

Cancer Res. 2009 Mar 15;69(6):2531-9. doi: 10.1158/0008-5472.CAN-08-3126. Epub 2009 Mar 3.

28.

Online resource for theoretical study of hydration of biopolymers.

Sobolev EV, Sobolev OV, Tikhonov DA.

SAR QSAR Environ Res. 2008 Apr-Jun;19(3-4):303-15. doi: 10.1080/10629360802083707.

PMID:
18484500
29.

Importance of donor- and recipient-derived selectins in cardiac allograft rejection.

Izawa A, Ueno T, Jurewicz M, Ito T, Tanaka K, Takahashi M, Ikeda U, Sobolev O, Fiorina P, Smith RN, Hynes RO, Abdi R.

J Am Soc Nephrol. 2007 Nov;18(11):2929-36. Epub 2007 Oct 10.

30.

Hydration of Hg2+ in aqueous solution studied by neutron diffraction with isotopic substitution.

Sobolev O, Cuello GJ, Román-Ross G, Skipper NT, Charlet L.

J Phys Chem A. 2007 Jun 21;111(24):5123-5. Epub 2007 May 31.

PMID:
17536793
31.

Magnetic-field-induced spin excitations and renormalized spin gap of the underdoped La1.895Sr0.105CuO4 superconductor.

Chang J, Schnyder AP, Gilardi R, Rønnow HM, Pailhes S, Christensen NB, Niedermayer Ch, McMorrow DF, Hiess A, Stunault A, Enderle M, Lake B, Sobolev O, Momono N, Oda M, Ido M, Mudry C, Mesot J.

Phys Rev Lett. 2007 Feb 16;98(7):077004. Epub 2007 Feb 15.

PMID:
17359052

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