2013
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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:
Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature.
Science 2013 (online only)
(PDB IDs:
4ixq,
4ixr)
2012
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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:
Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode.
Proc Natl Acad Sci U S A. 2012 109:19103-7
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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:
Nanoflow electrospinning serial femtosecond crystallography.
Acta Cryst. 2012, D68:1584-7
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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:
Graphical tools for macromolecular crystallography in PHENIX.
J Appl Crystallogr. 2012 45:581-586.
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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:
Room temperature femtosecond X-ray diffraction of photosystem II microcrystals.
Proc Natl Acad Sci U S A. 2012, 109:9721-6
(PDB IDs:
4fby)
-
Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD:
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.
Acta Cryst. 2012, D68:381-390.
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Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD:
Towards automated crystallographic structure refinement with phenix.refine.
Acta Cryst. 2012, D68:352-367.
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Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N:
phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.
J Struct Funct Genomics. 2012 13:81-90
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Totir M, Echols N, Nanao M, Gee CL, Moskaleva A, Gradia S, Iavarone AT, Berger JM, May AP, Zubieta C, Alber T:
Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization.
PLoS One 2012, 7:e32498.
(PDB IDs:
3sbo
3nbu
3n6q
2hxy)
2011
- Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N,
Alber T:
Accessing protein conformational ensembles using room-temperature X-ray crystallography.
Proc Natl Acad Sci U S A. 2011 108:16247-52.
-
Adams PD, Afonine PV, Bunkoczi 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:
The Phenix software for automated determination of macromolecular
structures.
Methods 2011 (online only)
2010
- Lombana TN, Echols N, Good MC, Thomsen ND, Ng HL, Greenstein AE, Falick AM, King DS, Alber T:
Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknB.
Structure 2010 18:1667-77
(PDB IDs:
3ori
3ork
3orl
3orm
3oro
3orp
3ort)
- Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T:
Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
Protein Sci. 2010 19:1420-31
- Adams PD, Afonine PV, BunkA3czi G, Chen VB, Davis IW, Echols N,
Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty
NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC,
Zwart PH:
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Acta Cryst. 2010, D66:213-221.
2007
-
Fraser JS, Merlie JP, Echols N, Weisfield SR, Mignot T, Wemmer DE, Zusman DR, Alber T: An atypical receiver domain controls the dynamic polar localization of the Myxococcus xanthus social motility protein FrzS.
Mol Microbiol 2007 65:319-32
(PDB IDs:
2gkg
2i6f
2nt3
2nt4)
-
Cellitti J, Llinas M, Echols N, Shank EA, Gillespie B, Kwon E, Crowder SM, Dahlquist FW, Alber T, Marqusee S: Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment.
Protein Sci 2007 16:842-51
(PDB IDs:
2o4w
2o79
2o7a)
-
Greenstein AE, Echols N, Lombana TN, King DS, Alber T: Allosteric activation by dimerization of the PknD receptor Ser/Thr protein kinase from Mycobacterium tuberculosis.
J Biol Chem 2007 282:11427-35
2006
-
Greenstein AE, Grundner C, Echols N, Gay LM, Lombana TN, Miecskowski CA, Pullen KE, Sung PY, Alber T: Structure/function studies of Ser/Thr and Tyr protein phosphorylation in Mycobacterium tuberculosis.
J Mol Microbiol Biotechnol 2006 9:167-81
2005
-
Flores S, Echols N, Milburn D, Hespenheide B, Keating K, Lu J, Wells S, Yu EZ, Thorpe M, Gerstein M: The Database of Macromolecular Motions: new features added at the decade mark.
Nucleic Acids Res 2005 34:D296-301
-
Alexandrov V, Lehnert U, Echols N, Milburn D, Engelman D, Gerstein M: Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
Protein Sci 2005 14:633-43
2004
-
Wunderlich Z, Acton TB, Liu J, Kornhaber G, Everett J, Carter P, Lan N, Echols N, Gerstein M, Rost B, Montelione GT: The protein target list of the Northeast Structural Genomics Consortium.
Proteins 2004 56:181-7
-
Gerstein M, Echols N: Exploring the range of protein flexibility, from a structural proteomics perspective.
Curr Opin Chem Biol 2004 8:14-9
-
Goh CS, Lan N, Douglas SM, Wu B, Echols N, Smith A, Milburn D, Montelione GT, Zhao H, Gerstein M: Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.
J Mol Biol 2004 336:115-30
2003
-
Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M: ExpressYourself: A modular platform for processing and visualizing microarray data.
Nucleic Acids Res 2003 31:3477-82
-
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: SPINE 2: a system for collaborative structural proteomics within a federated database framework.
Nucleic Acids Res 2003 31:2833-8
-
Echols N, Milburn D, Gerstein M: MolMovDB: analysis and visualization of conformational change and structural flexibility.
Nucleic Acids Res 2003 31:478-82
2002
-
Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M: GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.
Nucleic Acids Res 2002 30:4574-82
-
Krebs WG, Alexandrov V, Wilson CA, Echols N, Yu H, Gerstein M: Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.
Proteins 2002 48:682-95
-
Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M: SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.
Pharmacogenomics 2002 3:393-402
-
Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, Gerstein M: Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
Nucleic Acids Res 2002 30:2515-23
-
Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein M: A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution.
J Mol Biol 2002 316:409-19
-
Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M: Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.
Genome Res 2002 12:272-80
2001
-
Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M: An integrated approach for finding overlooked genes in yeast.
Nat Biotechnol 2001 20:58-63
-
Qian J, Stenger B, Wilson CA, Lin J, Jansen R, Teichmann SA, Park J, Krebs WG, Yu H, Alexandrov V, Echols N, Gerstein M: PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.
Nucleic Acids Res 2001 29:1750-64
-
Harrison PM, Echols N, Gerstein MB: Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome.
Nucleic Acids Res 2001 29:818-30