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Items: 1 to 20 of 74

1.

Structural biology data archiving - where we are and what lies ahead.

Kleywegt GJ, Velankar S, Patwardhan A.

FEBS Lett. 2018 May 10. doi: 10.1002/1873-3468.13086. [Epub ahead of print] Review.

PMID:
29749603
2.

The 3.5-Å CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase Vo Proton Channel.

Roh SH, Stam NJ, Hryc CF, Couoh-Cardel S, Pintilie G, Chiu W, Wilkens S.

Mol Cell. 2018 Mar 15;69(6):993-1004.e3. doi: 10.1016/j.molcel.2018.02.006. Epub 2018 Mar 8.

PMID:
29526695
3.

Validation of Structures in the Protein Data Bank.

Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ.

Structure. 2017 Dec 5;25(12):1916-1927. doi: 10.1016/j.str.2017.10.009. Epub 2017 Nov 22.

4.

Structural and Functional Impacts of ER Coactivator Sequential Recruitment.

Yi P, Wang Z, Feng Q, Chou CK, Pintilie GD, Shen H, Foulds CE, Fan G, Serysheva I, Ludtke SJ, Schmid MF, Hung MC, Chiu W, O'Malley BW.

Mol Cell. 2017 Sep 7;67(5):733-743.e4. doi: 10.1016/j.molcel.2017.07.026. Epub 2017 Aug 24.

PMID:
28844863
5.

Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM.

Roh SH, Hryc CF, Jeong HH, Fei X, Jakana J, Lorimer GH, Chiu W.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8259-8264. doi: 10.1073/pnas.1704725114. Epub 2017 Jul 14.

6.

Building bridges between cellular and molecular structural biology.

Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ.

Elife. 2017 Jul 6;6. pii: e25835. doi: 10.7554/eLife.25835.

7.

Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.

Dou H, Burrows DW, Baker ML, Ju T.

Biophys J. 2017 Jun 20;112(12):2479-2493. doi: 10.1016/j.bpj.2017.04.054.

8.

Trends in the Electron Microscopy Data Bank (EMDB).

Patwardhan A.

Acta Crystallogr D Struct Biol. 2017 Jun 1;73(Pt 6):503-508. doi: 10.1107/S2059798317004181. Epub 2017 Apr 20.

9.

An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump.

Wang Z, Fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, Du D.

Elife. 2017 Mar 29;6. pii: e24905. doi: 10.7554/eLife.24905.

10.

Accurate model annotation of a near-atomic resolution cryo-EM map.

Hryc CF, Chen DH, Afonine PV, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams PD, King JA, Schmid MF, Chiu W.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3103-3108. doi: 10.1073/pnas.1621152114. Epub 2017 Mar 7.

11.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK.

Structure. 2017 Mar 7;25(3):536-545. doi: 10.1016/j.str.2017.01.004. Epub 2017 Feb 9.

12.

Databases and Archiving for CryoEM.

Patwardhan A, Lawson CL.

Methods Enzymol. 2016;579:393-412. doi: 10.1016/bs.mie.2016.04.015. Epub 2016 Jun 16. Review.

13.

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

DiMaio F, Chiu W.

Methods Enzymol. 2016;579:255-76. doi: 10.1016/bs.mie.2016.06.003. Epub 2016 Aug 12. Review.

14.

The archiving and dissemination of biological structure data.

Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S.

Curr Opin Struct Biol. 2016 Oct;40:17-22. doi: 10.1016/j.sbi.2016.06.018. Epub 2016 Jul 21. Review.

15.

De Novo modeling in cryo-EM density maps with Pathwalking.

Chen M, Baldwin PR, Ludtke SJ, Baker ML.

J Struct Biol. 2016 Dec;196(3):289-298. doi: 10.1016/j.jsb.2016.06.004. Epub 2016 Jul 17.

16.

Quantifying Variability of Manual Annotation in Cryo-Electron Tomograms.

Hecksel CW, Darrow MC, Dai W, Galaz-Montoya JG, Chin JA, Mitchell PG, Chen S, Jakana J, Schmid MF, Chiu W.

Microsc Microanal. 2016 Jun;22(3):487-96. doi: 10.1017/S1431927616000799. Epub 2016 May 26.

17.

EMPIAR: a public archive for raw electron microscopy image data.

Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A.

Nat Methods. 2016 May;13(5):387-8. doi: 10.1038/nmeth.3806. Epub 2016 Mar 21. No abstract available.

PMID:
27067018
18.

Web-based volume slicer for 3D electron-microscopy data from EMDB.

Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A.

J Struct Biol. 2016 May;194(2):164-70. doi: 10.1016/j.jsb.2016.02.012. Epub 2016 Feb 10.

19.

The Electron Microscopy eXchange (EMX) initiative.

Marabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB, Carazo JM.

J Struct Biol. 2016 May;194(2):156-63. doi: 10.1016/j.jsb.2016.02.008. Epub 2016 Feb 9.

20.

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.

Pintilie G, Chen DH, Haase-Pettingell CA, King JA, Chiu W.

Biophys J. 2016 Feb 23;110(4):827-39. doi: 10.1016/j.bpj.2015.11.3522. Epub 2015 Dec 30.

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