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Items: 1 to 50 of 65

1.

Four steps for revealing and adjusting the 3D structure of aptamers in solution by small-angle X-ray scattering and computer simulation.

Tomilin FN, Moryachkov R, Shchugoreva I, Zabluda VN, Peters G, Platunov M, Spiridonova V, Melnichuk A, Atrokhova A, Zamay SS, Ovchinnikov SG, Zamay GS, Sokolov A, Zamay TN, Berezovski MV, Kichkailo AS.

Anal Bioanal Chem. 2019 Aug 8. doi: 10.1007/s00216-019-02045-0. [Epub ahead of print]

PMID:
31396648
2.

A demonstration of unsupervised machine learning in species delimitation.

Derkarabetian S, Castillo S, Koo PK, Ovchinnikov S, Hedin M.

Mol Phylogenet Evol. 2019 Jul 16;139:106562. doi: 10.1016/j.ympev.2019.106562. [Epub ahead of print]

PMID:
31323334
3.

Protein interaction networks revealed by proteome coevolution.

Cong Q, Anishchenko I, Ovchinnikov S, Baker D.

Science. 2019 Jul 12;365(6449):185-189. doi: 10.1126/science.aaw6718. Epub 2019 Jul 11.

PMID:
31296772
4.

A structural and data-driven approach to engineering a plant cytochrome P450 enzyme.

Li D, Ma Y, Zhou Y, Gou J, Zhong Y, Zhao L, Han L, Ovchinnikov S, Ma L, Huang S, Greisen P, Shang Y.

Sci China Life Sci. 2019 Jul;62(7):873-882. doi: 10.1007/s11427-019-9538-3. Epub 2019 May 21.

PMID:
31119558
5.

Development of a dual-functional conjugate of antigenic peptide and Fc-III mimetics (DCAF) for targeted antibody blocking.

Zhang L, Shen H, Gong Y, Pang X, Yi M, Guo L, Li J, Arroyo S, Lu X, Ovchinnikov S, Cheng G, Liu X, Jiang X, Feng S, Deng H.

Chem Sci. 2019 Jan 28;10(11):3271-3280. doi: 10.1039/c8sc05273e. eCollection 2019 Mar 21.

6.

Effect of Oxygen Nonstoichiometry on Electrical Conductivity and Thermopower of Gd0.2Sr0.8FeO3-δ Ferrite Samples.

Dudnikov V, Orlov Y, Fedorov A, Solovyov L, Vereshchagin S, Burkov A, Novikov S, Ovchinnikov S.

Materials (Basel). 2018 Dec 26;12(1). pii: E74. doi: 10.3390/ma12010074.

7.

Estimation of the thermal and photochemical stabilities of pheromones.

Tomilin FN, Fedorov AS, Artyushenko PV, Ovchinnikov SG, Ovchinnikova TM, Tsikalova PE, Soukhovolsky VG.

J Mol Model. 2018 Oct 24;24(11):323. doi: 10.1007/s00894-018-3859-5.

PMID:
30357483
8.

De novo design of a fluorescence-activating β-barrel.

Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, Vaughan JC, Stoddard BL, Baker D.

Nature. 2018 Sep;561(7724):485-491. doi: 10.1038/s41586-018-0509-0. Epub 2018 Sep 12.

9.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium, Crivelli SN.

Sci Rep. 2018 Jul 2;8(1):9939. doi: 10.1038/s41598-018-26812-8.

10.

Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis.

Sutherland MC, Jarodsky JM, Ovchinnikov S, Baker D, Kranz RG.

J Mol Biol. 2018 Apr 13;430(8):1065-1080. doi: 10.1016/j.jmb.2018.01.022. Epub 2018 Mar 5.

11.

Protein homology model refinement by large-scale energy optimization.

Park H, Ovchinnikov S, Kim DE, DiMaio F, Baker D.

Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3054-3059. doi: 10.1073/pnas.1719115115. Epub 2018 Mar 5.

12.

Protein structure prediction using Rosetta in CASP12.

Ovchinnikov S, Park H, Kim DE, DiMaio F, Baker D.

Proteins. 2018 Mar;86 Suppl 1:113-121. doi: 10.1002/prot.25390. Epub 2017 Oct 8.

PMID:
28940798
13.

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12.

Park H, Kim DE, Ovchinnikov S, Baker D, DiMaio F.

Proteins. 2018 Mar;86 Suppl 1:283-291. doi: 10.1002/prot.25387. Epub 2017 Oct 16.

14.

Origins of coevolution between residues distant in protein 3D structures.

Anishchenko I, Ovchinnikov S, Kamisetty H, Baker D.

Proc Natl Acad Sci U S A. 2017 Aug 22;114(34):9122-9127. doi: 10.1073/pnas.1702664114. Epub 2017 Aug 7.

15.

Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3.

Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M.

Nature. 2017 Aug 17;548(7667):352-355. doi: 10.1038/nature23314. Epub 2017 Jul 6.

16.

Applications of contact predictions to structural biology.

Simkovic F, Ovchinnikov S, Baker D, Rigden DJ.

IUCrJ. 2017 Apr 18;4(Pt 3):291-300. doi: 10.1107/S2052252517005115. eCollection 2017 May 1. Review.

17.

Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.

Ekiert DC, Bhabha G, Isom GL, Greenan G, Ovchinnikov S, Henderson IR, Cox JS, Vale RD.

Cell. 2017 Apr 6;169(2):273-285.e17. doi: 10.1016/j.cell.2017.03.019.

18.

Overcoming an optimization plateau in the directed evolution of highly efficient nerve agent bioscavengers.

Goldsmith M, Aggarwal N, Ashani Y, Jubran H, Greisen PJ, Ovchinnikov S, Leader H, Baker D, Sussman JL, Goldenzweig A, Fleishman SJ, Tawfik DS.

Protein Eng Des Sel. 2017 Apr 1;30(4):333-345. doi: 10.1093/protein/gzx003.

PMID:
28159998
19.

Protein structure determination using metagenome sequence data.

Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D.

Science. 2017 Jan 20;355(6322):294-298. doi: 10.1126/science.aah4043.

20.

Ultraviolet fluorescence of coelenteramide and coelenteramide-containing fluorescent proteins. Experimental and theoretical study.

Alieva RR, Tomilin FN, Kuzubov AA, Ovchinnikov SG, Kudryasheva NS.

J Photochem Photobiol B. 2016 Sep;162:318-323. doi: 10.1016/j.jphotobiol.2016.07.004. Epub 2016 Jul 5.

PMID:
27400455
21.

Structural insights into SAM domain-mediated tankyrase oligomerization.

DaRosa PA, Ovchinnikov S, Xu W, Klevit RE.

Protein Sci. 2016 Sep;25(9):1744-52. doi: 10.1002/pro.2968. Epub 2016 Jul 4.

22.

[ANESTHESIA DURING THE SEPARATION OF THE FETUS IN FETU IN A 2 DAYS-LIFE CHILD WITH ACCOMPANYING NON-CORRECTED CRITICAL CONGENITAL HEART DISEASE (CHD)].

Agavelyan EG, Svarinskaya EM, Ovchinnikov SV.

Anesteziol Reanimatol. 2016 Jan-Feb;61(1):47-51. Russian.

PMID:
27192856
23.

Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases.

Safarian S, Rajendran C, Müller H, Preu J, Langer JD, Ovchinnikov S, Hirose T, Kusumoto T, Sakamoto J, Michel H.

Science. 2016 Apr 29;352(6285):583-6. doi: 10.1126/science.aaf2477.

24.

Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11.

Ovchinnikov S, Park H, Kim DE, Liu Y, Wang RY, Baker D.

Proteins. 2016 Sep;84 Suppl 1:181-8. doi: 10.1002/prot.25006. Epub 2016 Mar 6.

25.

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.

Ovchinnikov S, Kim DE, Wang RY, Liu Y, DiMaio F, Baker D.

Proteins. 2016 Sep;84 Suppl 1:67-75. doi: 10.1002/prot.24974. Epub 2016 Feb 24.

26.

Catalytic efficiencies of directly evolved phosphotriesterase variants with structurally different organophosphorus compounds in vitro.

Goldsmith M, Eckstein S, Ashani Y, Greisen P Jr, Leader H, Sussman JL, Aggarwal N, Ovchinnikov S, Tawfik DS, Baker D, Thiermann H, Worek F.

Arch Toxicol. 2016 Nov;90(11):2711-2724. Epub 2015 Nov 26.

PMID:
26612364
27.

Large-scale determination of previously unsolved protein structures using evolutionary information.

Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D.

Elife. 2015 Sep 3;4:e09248. doi: 10.7554/eLife.09248.

28.

Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4.

Antala S, Ovchinnikov S, Kamisetty H, Baker D, Dempski RE.

J Biol Chem. 2015 Jul 17;290(29):17796-805. doi: 10.1074/jbc.M114.617613. Epub 2015 May 13.

29.

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

Ovchinnikov S, Kamisetty H, Baker D.

Elife. 2014 May 1;3:e02030. doi: 10.7554/eLife.02030.

30.

Methane oxidation over A-site ordered and disordered Sr(0.8)Gd(0.2)CoO(3-δ) perovskites.

Vereshchagin SN, Solovyov LA, Rabchevskii EV, Dudnikov VA, Ovchinnikov SG, Anshits AG.

Chem Commun (Camb). 2014 Jun 11;50(46):6112-5. doi: 10.1039/c4cc00913d.

PMID:
24777361
31.

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.

Kamisetty H, Ovchinnikov S, Baker D.

Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15674-9. doi: 10.1073/pnas.1314045110. Epub 2013 Sep 5. Erratum in: Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18734.

32.

Quantum critical point and spin fluctuations in lower-mantle ferropericlase.

Lyubutin IS, Struzhkin VV, Mironovich AA, Gavriliuk AG, Naumov PG, Lin JF, Ovchinnikov SG, Sinogeikin S, Chow P, Xiao Y, Hemley RJ.

Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7142-7. doi: 10.1073/pnas.1304827110. Epub 2013 Apr 15.

34.

[Stability of lepidopterous pheromone molecules of forest insects to environmental factors].

Tomilin FN, Osina OV, Kuzubov AA, Ovchinnikov SG, Volkova PE, Ovchinnikova TM, Sukhovol'skiĭ VG.

Biofizika. 2011 Jul-Aug;56(4):714-22. Russian.

PMID:
21950075
35.

Intermediate-spin state of a 3d ion in the octahedral environment and generalization of the Tanabe-Sugano diagrams.

Lamonova KV, Zhitlukhina ES, Babkin RY, Orel SM, Ovchinnikov SG, Pashkevich YG.

J Phys Chem A. 2011 Nov 24;115(46):13596-604. doi: 10.1021/jp2071265. Epub 2011 Oct 21.

PMID:
21936547
36.

From underdoped to overdoped cuprates: two quantum phase transitions.

Ovchinnikov SG, Shneyder EI, Korshunov MM.

J Phys Condens Matter. 2011 Feb 2;23(4):045701. doi: 10.1088/0953-8984/23/4/045701. Epub 2011 Jan 12.

PMID:
21406893
37.

[Usage of the neutral anolyte for trophic ulcer treatment in patients with postthrombophlebitic syndrome].

Efimenko NA, Chernekhovskaia NE, Ovchinnikov SI, Chomaeva AA.

Voen Med Zh. 2010 Oct;331(10):28-32. Russian.

PMID:
21254582
38.

Creating and manipulating vortices in atomic wave functions with short electric field pulses.

Ovchinnikov SY, Sternberg JB, Macek JH, Lee TG, Schultz DR.

Phys Rev Lett. 2010 Nov 12;105(20):203005. Epub 2010 Nov 12.

PMID:
21231229
39.

Theory of deep minima in (e,2e) measurements of triply differential cross sections.

Macek JH, Sternberg JB, Ovchinnikov SY, Briggs JS.

Phys Rev Lett. 2010 Jan 22;104(3):033201. Epub 2010 Jan 20.

PMID:
20366640
40.

The Fermi surface and the role of electronic correlations in Sm(2-x)Ce(x)CuO4.

Korshunov MM, Zakharova EV, Nekrasov IA, Pchelkina ZV, Ovchinnikov SG.

J Phys Condens Matter. 2010 Jan 13;22(1):015701. doi: 10.1088/0953-8984/22/1/015701. Epub 2009 Dec 2.

PMID:
21386232
41.

[The mechanism of formation of emitter by fluorescence of calcium-discharged obelin].

Tomilin FN, Antipina LIu, Vysotskiĭ ES, Ovchinnikov SG, Gitel'zon II.

Biofizika. 2009 Jul-Aug;54(4):630-7. Russian.

PMID:
19795783
42.

Origin, evolution, and imaging of vortices in atomic processes.

Macek JH, Sternberg JB, Ovchinnikov SY, Lee TG, Schultz DR.

Phys Rev Lett. 2009 Apr 10;102(14):143201. Epub 2009 Apr 10.

PMID:
19392436
43.

Fluorescence of calcium-discharged obelin: the structure and molecular mechanism of emitter formation.

Tomilin FN, Antipina LY, Vysotski ES, Ovchinnikov SG, Gitelzon II.

Dokl Biochem Biophys. 2008 Sep-Oct;422:279-84. No abstract available.

PMID:
19024558
44.

Atypical quantum confinement effect in silicon nanowires.

Sorokin PB, Avramov PV, Chernozatonskii LA, Fedorov DG, Ovchinnikov SG.

J Phys Chem A. 2008 Oct 9;112(40):9955-64. doi: 10.1021/jp805069b. Epub 2008 Sep 11.

PMID:
18785695
45.

Geometric phases and quantum phase transitions in open systems.

Nesterov AI, Ovchinnikov SG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jul;78(1 Pt 2):015202. Epub 2008 Jul 18.

PMID:
18764008
46.

Novel pressure-induced magnetic transition in magnetite (Fe3O4).

Ding Y, Haskel D, Ovchinnikov SG, Tseng YC, Orlov YS, Lang JC, Mao HK.

Phys Rev Lett. 2008 Feb 1;100(4):045508. Epub 2008 Feb 1.

PMID:
18352301
47.

[The use of air-plasmatic flows in the complex treatment of lower extremity trophic ulcers].

Efimenko NA, Chernekhovskaia NE, Ovchinnikov SI.

Voen Med Zh. 2007 Mar;328(3):22-4. Russian. No abstract available.

PMID:
17580473
48.

Lattice vibrations in an α- and β-AgCuS superionic conductor: experimental time-of-flight inelastic neutron scattering studies.

Skomorokhov AN, Trots DM, Ovchinnikov SG, Fuess H.

J Phys Condens Matter. 2007 May 8;19(18):186228. doi: 10.1088/0953-8984/19/18/186228. Epub 2007 Apr 17.

PMID:
21691009
49.

Regge oscillations in integral cross sections for proton impact on atomic hydrogen.

Macek JH, Krstić PS, Ovchinnikov SY.

Phys Rev Lett. 2004 Oct 29;93(18):183203. Epub 2004 Oct 29.

PMID:
15525162
50.

[Etiological and pathogenetic mechanisms in development of craniosynostoses in children].

Ovchinnikov SN, Severgina ES, Lopatin AV.

Arkh Patol. 2003 May-Jun;65(3):54-8. Review. Russian.

PMID:
12879617

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