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Items: 1 to 50 of 54

1.

Interactive comparison and remediation of collections of macromolecular structures.

Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd JJ, Poon BK, Adams PD.

Protein Sci. 2018 Jan;27(1):182-194. doi: 10.1002/pro.3296. Epub 2017 Nov 11.

2.

Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA.

Buchko GW, Echols N, Flynn EM, Ng HL, Stephenson S, Kim HB, Myler PJ, Terwilliger TC, Alber T, Kim CY.

Biochemistry. 2017 Aug 1;56(30):4015-4027. doi: 10.1021/acs.biochem.7b00511. Epub 2017 Jul 25.

PMID:
28692281
3.

No observable conformational changes in PSII.

Sauter NK, Echols N, Adams PD, Zwart PH, Kern J, Brewster AS, Koroidov S, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Yano J, Yachandra VK.

Nature. 2016 May 19;533(7603):E1-2. doi: 10.1038/nature17983. No abstract available.

4.

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS.

Nat Methods. 2015 Oct;12(10):943-6. doi: 10.1038/nmeth.3541. Epub 2015 Aug 17.

5.

RNA Structure Refinement Using the ERRASER-Phenix Pipeline.

Chou FC, Echols N, Terwilliger TC, Das R.

Methods Mol Biol. 2016;1320:269-82. doi: 10.1007/978-1-4939-2763-0_17.

6.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures.

Morshed N, Echols N, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1147-58. doi: 10.1107/S1399004715004241. Epub 2015 Apr 25.

7.

Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns.

Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK.

Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):357-66. doi: 10.1107/S1399004714026145. Epub 2015 Jan 23.

8.

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.

9.

Improved crystal orientation and physical properties from single-shot XFEL stills.

Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Dec 1;70(Pt 12):3299-309. doi: 10.1107/S1399004714024134. Epub 2014 Nov 28.

10.

dxtbx: the diffraction experiment toolbox.

Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton AW, Echols N, Evans G, Sauter NK, Winter G.

J Appl Crystallogr. 2014 Jul 19;47(Pt 4):1459-1465. eCollection 2014 Aug 1.

11.

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK.

Nat Commun. 2014 Jul 9;5:4371. doi: 10.1038/ncomms5371.

12.

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement.

Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1346-56. doi: 10.1107/S1399004714003277. Epub 2014 Apr 30.

13.

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.

14.

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams PD, Sauter NK.

Nat Methods. 2014 May;11(5):545-8. doi: 10.1038/nmeth.2887. Epub 2014 Mar 16. Erratum in: Nat Methods. 2015 Jul;12(7):692.

15.

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.

16.

Ligand placement based on prior structures: the guided ligand-replacement method.

Klei HE, Moriarty NW, Echols N, Terwilliger TC, Baldwin ET, Pokross M, Posy S, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):134-43. doi: 10.1107/S1399004713030071. Epub 2013 Dec 25.

17.

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.

18.

Improved low-resolution crystallographic refinement with Phenix and Rosetta.

DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D.

Nat Methods. 2013 Nov;10(11):1102-4. doi: 10.1038/nmeth.2648. Epub 2013 Sep 29.

19.

New Python-based methods for data processing.

Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N.

Acta Crystallogr D Biol Crystallogr. 2013 Jul;69(Pt 7):1274-82. doi: 10.1107/S0907444913000863. Epub 2013 Jun 18.

20.

Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature.

Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J.

Science. 2013 Apr 26;340(6131):491-5. doi: 10.1126/science.1234273. Epub 2013 Feb 14.

21.

Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode.

Alonso-Mori R, Kern J, Gildea RJ, Sokaras D, Weng TC, Lassalle-Kaiser B, Tran R, Hattne J, Laksmono H, Hellmich J, Glöckner C, Echols N, Sierra RG, Schafer DW, Sellberg J, Kenney C, Herbst R, Pines J, Hart P, Herrmann S, Grosse-Kunstleve RW, Latimer MJ, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Zouni A, Messinger J, Glatzel P, Sauter NK, Yachandra VK, Yano J, Bergmann U.

Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19103-7. doi: 10.1073/pnas.1211384109. Epub 2012 Nov 5.

22.

Nanoflow electrospinning serial femtosecond crystallography.

Sierra RG, Laksmono H, Kern J, Tran R, Hattne J, Alonso-Mori R, Lassalle-Kaiser B, Glöckner C, Hellmich J, Schafer DW, Echols N, Gildea RJ, Grosse-Kunstleve RW, Sellberg J, McQueen TA, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Hampton CY, Starodub D, Loh ND, Sokaras D, Weng TC, Zwart PH, Glatzel P, Milathianaki D, White WE, Adams PD, Williams GJ, Boutet S, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK, Bogan MJ.

Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1584-7. doi: 10.1107/S0907444912038152. Epub 2012 Oct 18.

23.

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.

24.

Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.

Kern J, Alonso-Mori R, Hellmich J, Tran R, Hattne J, Laksmono H, Glöckner C, Echols N, Sierra RG, Sellberg J, Lassalle-Kaiser B, Gildea RJ, Glatzel P, Grosse-Kunstleve RW, Latimer MJ, McQueen TA, DiFiore D, Fry AR, Messerschmidt M, Miahnahri A, Schafer DW, Seibert MM, Sokaras D, Weng TC, Zwart PH, White WE, Adams PD, Bogan MJ, Boutet S, Williams GJ, Messinger J, Sauter NK, Zouni A, Bergmann U, Yano J, Yachandra VK.

Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):9721-6. doi: 10.1073/pnas.1204598109. Epub 2012 Jun 4.

25.

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.

Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):381-90. doi: 10.1107/S0907444911047834. Epub 2012 Mar 16.

26.

Towards automated crystallographic structure refinement with phenix.refine.

Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi: 10.1107/S0907444912001308. Epub 2012 Mar 16.

27.

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.

Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N.

J Struct Funct Genomics. 2012 Jun;13(2):81-90. doi: 10.1007/s10969-012-9129-3. Epub 2012 Mar 15.

28.

Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization.

Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T.

PLoS One. 2012;7(2):e32498. doi: 10.1371/journal.pone.0032498. Epub 2012 Feb 29.

29.

Accessing protein conformational ensembles using room-temperature X-ray crystallography.

Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T.

Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16247-52. doi: 10.1073/pnas.1111325108. Epub 2011 Sep 14.

30.

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.

31.

Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB.

Lombana TN, Echols N, Good MC, Thomsen ND, Ng HL, Greenstein AE, Falick AM, King DS, Alber T.

Structure. 2010 Dec 8;18(12):1667-77. doi: 10.1016/j.str.2010.09.019.

32.

Automated electron-density sampling reveals widespread conformational polymorphism in proteins.

Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T.

Protein Sci. 2010 Jul;19(7):1420-31. doi: 10.1002/pro.423.

33.

PHENIX: a comprehensive Python-based system for macromolecular structure solution.

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

Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. doi: 10.1107/S0907444909052925. Epub 2010 Jan 22.

34.

An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.

Fraser JS, Merlie JP Jr, Echols N, Weisfield SR, Mignot T, Wemmer DE, Zusman DR, Alber T.

Mol Microbiol. 2007 Jul;65(2):319-32. Epub 2007 Jun 15.

35.

Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment.

Cellitti J, Llinas M, Echols N, Shank EA, Gillespie B, Kwon E, Crowder SM, Dahlquist FW, Alber T, Marqusee S.

Protein Sci. 2007 May;16(5):842-51. Epub 2007 Mar 30.

36.

Allosteric activation by dimerization of the PknD receptor Ser/Thr protein kinase from Mycobacterium tuberculosis.

Greenstein AE, Echols N, Lombana TN, King DS, Alber T.

J Biol Chem. 2007 Apr 13;282(15):11427-35. Epub 2007 Jan 22.

37.

Structure/function studies of Ser/Thr and Tyr protein phosphorylation in Mycobacterium tuberculosis.

Greenstein AE, Grundner C, Echols N, Gay LM, Lombana TN, Miecskowski CA, Pullen KE, Sung PY, Alber T.

J Mol Microbiol Biotechnol. 2005;9(3-4):167-81. Review.

PMID:
16415590
38.

The Database of Macromolecular Motions: new features added at the decade mark.

Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D296-301.

39.

Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.

Alexandrov V, Lehnert U, Echols N, Milburn D, Engelman D, Gerstein M.

Protein Sci. 2005 Mar;14(3):633-43.

40.

The protein target list of the Northeast Structural Genomics Consortium.

Wunderlich Z, Acton TB, Liu J, Kornhaber G, Everett J, Carter P, Lan N, Echols N, Gerstein M, Rost B, Montelione GT.

Proteins. 2004 Aug 1;56(2):181-7. No abstract available.

PMID:
15211503
41.

Exploring the range of protein flexibility, from a structural proteomics perspective.

Gerstein M, Echols N.

Curr Opin Chem Biol. 2004 Feb;8(1):14-9. Review.

PMID:
15036151
42.

Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.

Goh CS, Lan N, Douglas SM, Wu B, Echols N, Smith A, Milburn D, Montelione GT, Zhao H, Gerstein M.

J Mol Biol. 2004 Feb 6;336(1):115-30.

PMID:
14741208
43.

ExpressYourself: A modular platform for processing and visualizing microarray data.

Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M.

Nucleic Acids Res. 2003 Jul 1;31(13):3477-82.

44.

SPINE 2: a system for collaborative structural proteomics within a federated database framework.

Goh CS, Lan N, Echols N, Douglas SM, Milburn D, Bertone P, Xiao R, Ma LC, Zheng D, Wunderlich Z, Acton T, Montelione GT, Gerstein M.

Nucleic Acids Res. 2003 Jun 1;31(11):2833-8.

45.

MolMovDB: analysis and visualization of conformational change and structural flexibility.

Echols N, Milburn D, Gerstein M.

Nucleic Acids Res. 2003 Jan 1;31(1):478-82.

46.

GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.

Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M.

Nucleic Acids Res. 2002 Oct 15;30(20):4574-82.

47.

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.

Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M.

Proteins. 2002 Sep 1;48(4):682-95.

PMID:
12211036
48.

SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.

Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M.

Pharmacogenomics. 2002 May;3(3):393-402.

PMID:
12052146
49.

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.

Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, Gerstein M.

Nucleic Acids Res. 2002 Jun 1;30(11):2515-23.

50.

A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.

Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein M.

J Mol Biol. 2002 Feb 22;316(3):409-19.

PMID:
11866506

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