Nathaniel Echols, Ph.D. - Publications

2008 University of California, Berkeley, Berkeley, CA 
Molecular Biology, General Biophysics, Microbiology Biology

52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Buchko GW, Echols N, Flynn EM, Ng H, Stephenson S, Kim HB, Myler PJ, Terwilliger TC, Alber T, Kim CY. Structural and biophysical characterization of the Mycobacterium tuberculosis protein Rv0577, a protein associated with neutral red staining of virulent tuberculosis strains and homolog of the Streptomyces coelicolor protein KbpA. Biochemistry. PMID 28692281 DOI: 10.1021/acs.biochem.7b00511  0.6
2016 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. No observable conformational changes in PSII. Nature. 533: E1-2. PMID 27193689 DOI: 10.1038/nature17983  0.6
2016 Chou FC, Echols N, Terwilliger TC, Das R. RNA structure refi nement using the erraser-phenix pipeline Methods in Molecular Biology. 1320: 269-282. DOI: 10.1007/978-1-4939-2763-0_17  0.6
2015 Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nature Methods. 12: 943-6. PMID 26280328 DOI: 10.1038/nmeth.3541  0.6
2015 Morshed N, Echols N, Adams PD. Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 71: 1147-58. PMID 25945580 DOI: 10.1107/S1399004715004241  0.6
2015 Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Acta Crystallographica. Section D, Biological Crystallography. 71: 357-66. PMID 25664747 DOI: 10.1107/S1399004714026145  0.6
2015 Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nature Methods. 12: 127-30. PMID 25532136 DOI: 10.1038/nmeth.3212  0.6
2014 Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD. Improved crystal orientation and physical properties from single-shot XFEL stills. Acta Crystallographica. Section D, Biological Crystallography. 70: 3299-309. PMID 25478847 DOI: 10.1107/S1399004714024134  0.6
2014 Parkhurst JM, Brewster AS, Fuentes-Montero L, Waterman DG, Hattne J, Ashton AW, Echols N, Evans G, Sauter NK, Winter G. dxtbx: the diffraction experiment toolbox. Journal of Applied Crystallography. 47: 1459-1465. PMID 25242914 DOI: 10.1107/S1600576714011996  0.6
2014 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, et al. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications. 5: 4371. PMID 25006873 DOI: 10.1038/ncomms5371  0.6
2014 Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. Acta Crystallographica. Section D, Biological Crystallography. 70: 1346-56. PMID 24816103 DOI: 10.1107/S1399004714003277  0.6
2014 Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD. Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 70: 1104-14. PMID 24699654 DOI: 10.1107/S1399004714001308  0.6
2014 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, et al. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods. 11: 545-8. PMID 24633409 DOI: 10.1038/nmeth.2887  0.6
2014 Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Automating crystallographic structure solution and refinement of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography. 70: 144-54. PMID 24419387 DOI: 10.1107/S139900471302748X  0.6
2014 Klei HE, Moriarty NW, Echols N, Terwilliger TC, Baldwin ET, Pokross M, Posy S, Adams PD. Ligand placement based on prior structures: the guided ligand-replacement method Acta Crystallographica Section D: Biological Crystallography. 70: 134-143. PMID 24419386 DOI: 10.1107/S1399004713030071  0.6
2013 Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ. Phaser.MRage: automated molecular replacement. Acta Crystallographica. Section D, Biological Crystallography. 69: 2276-86. PMID 24189240 DOI: 10.1107/S0907444913022750  0.6
2013 DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods. 10: 1102-4. PMID 24076763 DOI: 10.1038/nmeth.2648  0.6
2013 Sauter NK, Hattne J, Grosse-Kunstleve RW, Echols N. New Python-based methods for data processing. Acta Crystallographica. Section D, Biological Crystallography. 69: 1274-82. PMID 23793153 DOI: 10.1107/S0907444913000863  0.6
2013 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, et al. Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science (New York, N.Y.). 340: 491-5. PMID 23413188 DOI: 10.1126/science.1234273  0.6
2012 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, et al. Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode. Proceedings of the National Academy of Sciences of the United States of America. 109: 19103-7. PMID 23129631 DOI: 10.1073/pnas.1211384109  0.6
2012 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, et al. Nanoflow electrospinning serial femtosecond crystallography. Acta Crystallographica. Section D, Biological Crystallography. 68: 1584-7. PMID 23090408 DOI: 10.1107/S0907444912038152  0.6
2012 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. Journal of Applied Crystallography. 45: 581-586. PMID 22675231 DOI: 10.1107/S0021889812017293  0.6
2012 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, et al. Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proceedings of the National Academy of Sciences of the United States of America. 109: 9721-6. PMID 22665786 DOI: 10.1073/pnas.1204598109  0.6
2012 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 Crystallographica. Section D, Biological Crystallography. 68: 381-90. PMID 22505258 DOI: 10.1107/S0907444911047834  0.6
2012 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 Crystallographica. Section D, Biological Crystallography. 68: 352-67. PMID 22505256 DOI: 10.1107/S0907444912001308  0.6
2012 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. Journal of Structural and Functional Genomics. 13: 81-90. PMID 22418934 DOI: 10.1007/s10969-012-9129-3  0.6
2012 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. 7: e32498. PMID 22393408 DOI: 10.1371/journal.pone.0032498  0.6
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 Proceedings of the National Academy of Sciences of the United States of America. 108: 16247-16252. PMID 21918110 DOI: 10.1073/pnas.1111325108  0.6
2011 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, et al. The Phenix software for automated determination of macromolecular structures. Methods (San Diego, Calif.). 55: 94-106. PMID 21821126 DOI: 10.1016/j.ymeth.2011.07.005  0.6
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 (London, England : 1993). 18: 1667-77. PMID 21134645 DOI: 10.1016/j.str.2010.09.019  0.6
2010 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 Science : a Publication of the Protein Society. 19: 1420-31. PMID 20499387 DOI: 10.1002/pro.423  0.6
2010 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, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica. Section D, Biological Crystallography. 66: 213-21. PMID 20124702 DOI: 10.1107/S0907444909052925  0.6
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. Molecular Microbiology. 65: 319-32. PMID 17573816 DOI: 10.1111/j.1365-2958.2007.05785.x  0.6
2007 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 Science : a Publication of the Protein Society. 16: 842-51. PMID 17400926 DOI: 10.1110/ps.062628607  0.6
2007 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. The Journal of Biological Chemistry. 282: 11427-35. PMID 17242402 DOI: 10.1074/jbc.M610193200  0.6
2006 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 Research. 34: D296-301. PMID 16381870 DOI: 10.1093/nar/gkj046  0.6
2005 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. Journal of Molecular Microbiology and Biotechnology. 9: 167-81. PMID 16415590 DOI: 10.1159/000089645  0.6
2005 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 Science : a Publication of the Protein Society. 14: 633-43. PMID 15722444 DOI: 10.1110/ps.04882105  0.6
2004 Gerstein M, Echols N. Exploring the range of protein flexibility, from a structural proteomics perspective. Current Opinion in Chemical Biology. 8: 14-9. PMID 15036151 DOI: 10.1016/j.cbpa.2003.12.006  0.6
2004 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. Journal of Molecular Biology. 336: 115-30. PMID 14741208 DOI: 10.1016/j.jmb.2003.11.053  0.6
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 Research. 31: 3477-82. PMID 12824348 DOI: 10.1093/nar/gkg628  0.6
2003 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 Research. 31: 2833-8. PMID 12771210 DOI: 10.1093/nar/gkg397  0.6
2003 Echols N, Milburn D, Gerstein M. MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Research. 31: 478-82. PMID 12520056 DOI: 10.1093/nar/gkg104  0.6
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 Research. 30: 4574-82. PMID 12384605  0.6
2002 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. 48: 682-95. PMID 12211036 DOI: 10.1002/prot.10168  0.6
2002 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. 3: 393-402. PMID 12052146 DOI: 10.1517/14622416.3.3.393  0.6
2002 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 Research. 30: 2515-23. PMID 12034841  0.6
2002 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. Journal of Molecular Biology. 316: 409-19. PMID 11866506 DOI: 10.1006/jmbi.2001.5343  0.6
2002 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 Research. 12: 272-80. PMID 11827946 DOI: 10.1101/gr.207102  0.6
2002 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. Nature Biotechnology. 20: 58-63. PMID 11753363 DOI: 10.1038/nbt0102-58  0.6
2001 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 Research. 29: 1750-64. PMID 11292848  0.6
2001 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 Research. 29: 818-30. PMID 11160906  0.6
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