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    22833 Publications
    3073 Total Profiles
    24 Edited Profiles

    Adams, Paul

    TitleComputer Senior Scientist
    SchoolLawrence Berkeley National Lab
    DepartmentPhysical Biosciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/486-4225

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol. 2015; 3:153.
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      2. Sun L, Singh S, Joo M, Vega-Sanchez M, Ronald P, Simmons BA, Adams P, Auer M. Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy. Biotechnol Bioeng. 2016 Jan; 113(1):82-90.
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      3. Petzold CJ, Chan LJ, Nhan M, Adams PD. Analytics for Metabolic Engineering. Front Bioeng Biotechnol. 2015; 3:135.
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      4. 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. Nat Methods. 2015 Oct; 12(10):943-6.
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      5. Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS. Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Crystallogr D Biol Crystallogr. 2015 Aug 1; 71(Pt 8):1657-67.
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      6. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD. From deep TLS validation to ensembles of atomic models built from elemental motions. Acta Crystallogr D Biol Crystallogr. 2015 Aug 1; 71(Pt 8):1668-83.
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      7. Shih SC, Goyal G, Kim PW, Koutsoubelis N, Keasling JD, Adams PD, Hillson NJ, Singh AK. A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synth Biol. 2015 Oct 16; 4(10):1151-64.
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      8. George KW, Thompson MG, Kang A, Baidoo E, Wang G, Chan LJ, Adams PD, Petzold CJ, Keasling JD, Soon Lee T. Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli. Sci Rep. 2015; 5:11128.
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      9. Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW. NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nat Struct Mol Biol. 2015 Jun 3; 22(6):433-4.
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      10. Morshed N, Echols N, Adams PD. Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2015 May; 71(Pt 5):1147-58.
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      11. González Fernández-Niño SM, Smith-Moritz AM, Chan LJ, Adams PD, Heazlewood JL, Petzold CJ. Standard flow liquid chromatography for shotgun proteomics in bioenergy research. Front Bioeng Biotechnol. 2015; 3:44.
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      12. Ebert B, Rautengarten C, Guo X, Xiong G, Stonebloom S, Smith-Moritz AM, Herter T, Chan LJ, Adams PD, Petzold CJ, Pauly M, Willats WG, Heazlewood JL, Scheller HV. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis. Plant Cell. 2015 Apr; 27(4):1218-27.
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      13. Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD. FEM: feature-enhanced map. Acta Crystallogr D Biol Crystallogr. 2015 Mar 1; 71(Pt 3):646-66.
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      14. 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 Crystallogr D Biol Crystallogr. 2015 Feb; 71(Pt 2):357-66.
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      15. Alonso-Gutierrez J, Kim EM, Batth TS, Cho N, Hu Q, Chan LJ, Petzold CJ, Hillson NJ, Adams PD, Keasling JD, Garcia Martin H, Lee TS. Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering. Metab Eng. 2015 Mar; 28:123-33.
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      16. 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. Nat Methods. 2015 Feb; 12(2):127-30.
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      17. Shih SC, Gach PC, Sustarich J, Simmons BA, Adams PD, Singh S, Singh AK. A droplet-to-digital (D2D) microfluidic device for single cell assays. Lab Chip. 2014 Dec 3; 15(1):225-36.
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      18. Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):17887-92.
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      19. Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD. Improved crystal orientation and physical properties from single-shot XFEL stills. Acta Crystallogr D Biol Crystallogr. 2014 Dec 1; 70(Pt 12):3299-309.
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      20. McAndrew R, Pruitt RN, Kamita SG, Pereira JH, Majumdar D, Hammock BD, Adams PD, Ronald PC. Structure of the OsSERK2 leucine-rich repeat extracellular domain. Acta Crystallogr D Biol Crystallogr. 2014 Nov; 70(Pt 11):3080-6.
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      21. Poust S, Yoon I, Adams PD, Katz L, Petzold CJ, Keasling JD. Understanding the Role of Histidine in the GHSxG Acyltransferase Active Site Motif: Evidence for Histidine Stabilization of the Malonyl-Enzyme Intermediate. PLoS One. 2014; 9(10):e109421.
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      22. Rhee M, Light YK, Yilmaz S, Adams PD, Saxena D, Meagher RJ, Singh AK. Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. Lab Chip. 2014 Dec 7; 14(23):4533-9.
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      23. Urzhumtsev A, Afonine PV, Lunin VY, Terwilliger TC, Adams PD. Metrics for comparison of crystallographic maps. Acta Crystallogr D Biol Crystallogr. 2014 Oct 1; 70(Pt 10):2593-606.
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      24. Haushalter RW, Kim W, Chavkin TA, The L, Garber ME, Nhan M, Adams PD, Petzold CJ, Katz L, Keasling JD. Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties. Metab Eng. 2014 Sep 22; 26C:111-118.
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      25. Hagen A, Poust S, de Rond T, Yuzawa S, Katz L, Adams PD, Petzold CJ, Keasling JD. In vitro analysis of carboxyacyl substrate tolerance in the loading and first extension modules of borrelidin polyketide synthase. Biochemistry. 2014 Sep 30; 53(38):5975-7.
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      26. Batth TS, Singh P, Ramakrishnan VR, Sousa MM, Chan LJ, Tran HM, Luning EG, Pan EH, Vuu KM, Keasling JD, Adams PD, Petzold CJ. A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins. Metab Eng. 2014 Sep 7; 26C:48-56.
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      27. Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W. An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nat Commun. 2014; 5:4808.
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      28. Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG. A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities. PLoS Comput Biol. 2014 Sep; 10(9):e1003827.
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      29. Rennie EA, Ebert B, Miles GP, Cahoon RE, Christiansen KM, Stonebloom S, Khatab H, Twell D, Petzold CJ, Adams PD, Dupree P, Heazlewood JL, Cahoon EB, Scheller HV. Identification of a Sphingolipid a-Glucuronosyltransferase That Is Essential for Pollen Function in Arabidopsis. Plant Cell. 2014 Aug; 26(8):3314-25.
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      30. Pereira JH, Petchprayoon C, Hoepker AC, Moriarty NW, Fink SJ, Cecere G, Paterson I, Adams PD, Marriott G. Structural and biochemical studies of actin in complex with synthetic macrolide tail analogues. ChemMedChem. 2014 Oct; 9(10):2286-93.
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      31. Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. Phylogenomically Guided Identification of Industrially Relevant GH1 ß-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry. ACS Chem Biol. 2014 Sep 19; 9(9):2082-91.
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      32. 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. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun. 2014; 5:4371.
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      33. Lao J, Oikawa A, Bromley JR, McInerney P, Suttangkakul A, Smith-Moritz AM, Plahar H, Chiu TY, González Fernández-Niño SM, Ebert B, Yang F, Christiansen KM, Hansen SF, Stonebloom S, Adams PD, Ronald PC, Hillson NJ, Hadi MZ, Vega-Sánchez ME, Loqué D, Scheller HV, Heazlewood JL. The plant glycosyltransferase clone collection for functional genomics. Plant J. 2014 Aug; 79(3):517-29.
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      34. Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A. Development of a Native Escherichia coli Induction System for Ionic Liquid Tolerance. PLoS One. 2014; 9(7):e101115.
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      35. Dougherty MJ, Tran HM, Stavila V, Knierim B, George A, Auer M, Adams PD, Hadi MZ. Cellulosic biomass pretreatment and sugar yields as a function of biomass particle size. PLoS One. 2014; 9(6):e100836.
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      36. Kung Y, McAndrew RP, Xie X, Liu CC, Pereira JH, Adams PD, Keasling JD. Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase. Structure. 2014 Jul 8; 22(7):1028-36.
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      37. Moriarty NW, Tronrud DE, Adams PD, Karplus PA. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. FEBS J. 2014 Sep; 281(18):4061-71.
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      38. Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Rapid Kinetic Characterization of Glycosyl Hydrolases Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS). ACS Chem Biol. 2014 Jul 18; 9(7):1470-9.
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      39. George KW, Chen A, Jain A, Batth TS, Baidoo EE, Wang G, Adams PD, Petzold CJ, Keasling JD, Lee TS. Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production. Biotechnol Bioeng. 2014 Aug; 111(8):1648-58.
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      40. Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. Acta Crystallogr D Biol Crystallogr. 2014 May; 70(Pt 5):1346-56.
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      41. 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 Crystallogr D Biol Crystallogr. 2014 Apr 1; 70(Pt 4):1104-14.
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      42. 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. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat Methods. 2014 May; 11(5):545-8.
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      43. Wall ME, Adams PD, Fraser JS, Sauter NK. Diffuse x-ray scattering to model protein motions. Structure. 2014 Feb 4; 22(2):182-4.
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      44. Parsons HT, Weinberg CS, Macdonald LJ, Adams PD, Petzold CJ, Strabala TJ, Wagner A, Heazlewood JL. Golgi Enrichment and Proteomic Analysis of Developing Pinus radiata Xylem by Free-Flow Electrophoresis. PLoS One. 2013; 8(12):e84669.
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      45. 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 Crystallogr D Biol Crystallogr. 2014 Jan; 70(Pt 1):144-54.
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      46. 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 Crystallogr D Biol Crystallogr. 2014 Jan; 70(Pt 1):134-43.
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      47. Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal ß-glucosidase production. Front Microbiol. 2013; 4:365.
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      48. Ito J, Herter T, Baidoo EE, Lao J, Vega-Sánchez ME, Michelle Smith-Moritz A, Adams PD, Keasling JD, Usadel B, Petzold CJ, Heazlewood JL. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry. Anal Biochem. 2014 Mar 1; 448:14-22.
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      49. Chen Z, Pereira JH, Liu H, Tran HM, Hsu NS, Dibble D, Singh S, Adams PD, Sapra R, Hadi MZ, Simmons BA, Sale KL. Improved Activity of a Thermophilic Cellulase, Cel5A, from Thermotoga maritima on Ionic Liquid Pretreated Switchgrass. PLoS One. 2013; 8(11):e79725.
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      50. Javidpour P, Pereira JH, Goh EB, McAndrew RP, Ma SM, Friedland GD, Keasling JD, Chhabra SR, Adams PD, Beller HR. Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions. Appl Environ Microbiol. 2014 Jan; 80(2):497-505.
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      51. Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol. 2013 Nov; 31(11):1039-46.
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      52. Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Hung LW. Model morphing and sequence assignment after molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013 Nov; 69(Pt 11):2244-50.
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      53. Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ. Phaser.MRage: automated molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013 Nov; 69(Pt 11):2276-86.
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      54. Dimaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nat Methods. 2013 Nov; 10(11):1102-4.
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      55. Nwachukwu JC, Southern MR, Kiefer JR, Afonine PV, Adams PD, Terwilliger TC, Nettles KW. Improved crystallographic structures using extensive combinatorial refinement. Structure. 2013 Nov 5; 21(11):1923-30.
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      56. Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proc Natl Acad Sci U S A. 2013 Jul 23; 110(30):12301-6.
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      57. Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams PD, Sale KL, Hadi MZ, Simmons BA, Kent MS, Tullman-Ercek D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnol Biofuels. 2013; 6(1):93.
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      58. Chandrasekaran A, Deng K, Koh CY, Takasuka T, Bergeman LF, Fox BG, Adams PD, Singh AK. A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres. Chem Commun (Camb). 2013 Jun 18; 49(48):5441-3.
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      59. Alonso-Gutierrez J, Chan R, Batth TS, Adams PD, Keasling JD, Petzold CJ, Lee TS. Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production. Metab Eng. 2013 Sep; 19:33-41.
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      60. Chang C, Sustarich J, Bharadwaj R, Chandrasekaran A, Adams PD, Singh AK. Droplet-based microfluidic platform for heterogeneous enzymatic assays. Lab Chip. 2013 May 7; 13(9):1817-22.
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      61. McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons BA, Adams PD. From soil to structure, a novel dimeric ß-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. J Biol Chem. 2013 May 24; 288(21):14985-92.
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      62. Chiniquy D, Varanasi P, Oh T, Harholt J, Katnelson J, Singh S, Auer M, Simmons B, Adams PD, Scheller HV, Ronald PC. Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Front Plant Sci. 2013; 4:83.
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      63. Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A. Bulk-solvent and overall scaling revisited: faster calculations, improved results. Acta Crystallogr D Biol Crystallogr. 2013 Apr; 69(Pt 4):625-34.
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      64. Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annu Rev Biophys. 2013; 42:265-87.
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      65. 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 Apr 26; 340(6131):491-5.
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      66. Varanasi P, Singh P, Auer M, Adams PD, Simmons BA, Singh S. Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnol Biofuels. 2013; 6(1):14.
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      67. Read RJ, Adams PD, McCoy AJ. Intensity statistics in the presence of translational noncrystallographic symmetry. Acta Crystallogr D Biol Crystallogr. 2013 Feb; 69(Pt 2):176-83.
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      68. Burnley BT, Afonine PV, Adams PD, Gros P. Modelling dynamics in protein crystal structures by ensemble refinement. Elife. 2012; 1:e00311.
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      69. 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 Nov 20; 109(47):19103-7.
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      70. 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 Crystallogr D Biol Crystallogr. 2012 Nov; 68(Pt 11):1584-7.
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      71. Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling JD. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng. 2012 Nov; 14(6):653-60.
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      72. Pereira JH, Goh EB, Keasling JD, Beller HR, Adams PD. Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus. Acta Crystallogr D Biol Crystallogr. 2012 Oct; 68(Pt 10):1320-8.
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      73. Varanasi P, Singh P, Arora R, Adams PD, Auer M, Simmons BA, Singh S. Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Bioresour Technol. 2012 Dec; 126:156-61.
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      74. McClendon SD, Batth T, Petzold CJ, Adams PD, Simmons BA, Singer SW. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels. 2012; 5(1):54.
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      75. Dougherty MJ, D'haeseleer P, Hazen TC, Simmons BA, Adams PD, Hadi MZ. Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization. BMC Biotechnol. 2012; 12:38.
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      76. Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Grosse-Kunstleve RW, Hung LW. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. Acta Crystallogr D Biol Crystallogr. 2012 Jul; 68(Pt 7):861-70.
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      77. McKee AE, Rutherford BJ, Chivian DC, Baidoo EK, Juminaga D, Kuo D, Benke PI, Dietrich JA, Ma SM, Arkin AP, Petzold CJ, Adams PD, Keasling JD, Chhabra SR. Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. Microb Cell Fact. 2012; 11:79.
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      78. Brunger AT, Adams PD, Fromme P, Fromme R, Levitt M, Schröder GF. Improving the accuracy of macromolecular structure refinement at 7 Å resolution. Structure. 2012 Jun 6; 20(6):957-66.
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      79. 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 Jun 19; 109(25):9721-6.
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      80. Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams PD, Arkin AP, Keasling JD, Blanch HW, Simmons BA, Sale KL, Chivian D, Chhabra SR. Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. J Biol Chem. 2012 Jul 20; 287(30):25335-43.
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      81. Grosse-Kunstleve RW, Terwilliger TC, Sauter NK, Adams PD. Automatic Fortran to C++ conversion with FABLE. Source Code Biol Med. 2012; 7(1):5.
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      82. Gifford LK, Carter LG, Gabanyi MJ, Berman HM, Adams PD. The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. J Struct Funct Genomics. 2012 Jun; 13(2):57-62.
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      83. Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams PD, Petzold CJ. Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics. 2012 Apr; 12(8):1289-99.
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      84. Deng K, George KW, Reindl W, Keasling JD, Adams PD, Lee TS, Singh AK, Northen TR. Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme. Rapid Commun Mass Spectrom. 2012 Mar 30; 26(6):611-5.
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      85. 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 Crystallogr D Biol Crystallogr. 2012 Apr; 68(Pt 4):352-67.
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      86. 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 Crystallogr D Biol Crystallogr. 2012 Apr; 68(Pt 4):381-90.
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      87. Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, Levitt M, Schröder GF. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Crystallogr D Biol Crystallogr. 2012 Apr; 68(Pt 4):391-403.
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      88. 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 Jun; 13(2):81-90.
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      89. Groff D, Benke PI, Batth TS, Bokinsky G, Petzold CJ, Adams PD, Keasling JD. Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars. Appl Environ Microbiol. 2012 Apr; 78(7):2221-9.
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      90. Pereira JH, Ralston CY, Douglas NR, Kumar R, Lopez T, McAndrew RP, Knee KM, King JA, Frydman J, Adams PD. Mechanism of nucleotide sensing in group II chaperonins. EMBO J. 2012 Feb 1; 31(3):731-40.
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      91. McAndrew RP, Peralta-Yahya PP, DeGiovanni A, Pereira JH, Hadi MZ, Keasling JD, Adams PD. Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production. Structure. 2011 Dec 7; 19(12):1876-84.
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      92. Perera PN, Schmidt M, Chiang VL, Schuck PJ, Adams PD. Raman-spectroscopy-based noninvasive microanalysis of native lignin structure. Anal Bioanal Chem. 2012 Jan; 402(2):983-7.
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      93. Read RJ, Adams PD, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. A new generation of crystallographic validation tools for the protein data bank. Structure. 2011 Oct 12; 19(10):1395-412.
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      94. 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. The Phenix software for automated determination of macromolecular structures. Methods. 2011 Sep; 55(1):94-106.
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      95. Perera PN, Schmidt M, Schuck PJ, Adams PD. Blind image analysis for the compositional and structural characterization of plant cell walls. Anal Chim Acta. 2011 Sep 30; 702(2):172-7.
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      96. Chandrashekar R, Salem O, Krizova H, McFeeters R, Adams PD. A switch I mutant of Cdc42 exhibits less conformational freedom. Biochemistry. 2011 Jul 19; 50(28):6196-207.
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      97. Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics. 2011 Jul; 12(2):45-54.
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      98. Grosse-Kunstleve RW, Wong B, Mustyakimov M, Adams PD. Exact direct-space asymmetric units for the 230 crystallographic space groups. Acta Crystallogr A. 2011 May; 67(Pt 3):269-75.
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      99. Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams PD, Keasling JD, Lee TS, Mukhopadhyay A, Petzold CJ. Targeted proteomics for metabolic pathway optimization: application to terpene production. Metab Eng. 2011 Mar; 13(2):194-203.
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      100. Schmidt M, Perera P, Schwartzberg AM, Adams PD, Schuck PJ. Label-free in situ imaging of lignification in plant cell walls. J Vis Exp. 2010; (45).
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      101. Bharadwaj R, Chen Z, Datta S, Holmes BM, Sapra R, Simmons BA, Adams PD, Singh AK. Microfluidic glycosyl hydrolase screening for biomass-to-biofuel conversion. Anal Chem. 2010 Nov 15; 82(22):9513-20.
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      102. Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD. Joint X-ray and neutron refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr. 2010 Nov; 66(Pt 11):1153-63.
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      103. Bruning JB, Parent AA, Gil G, Zhao M, Nowak J, Pace MC, Smith CL, Afonine PV, Adams PD, Katzenellenbogen JA, Nettles KW. Coupling of receptor conformation and ligand orientation determine graded activity. Nat Chem Biol. 2010 Nov; 6(11):837-43.
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      104. Bharadwaj R, Wong A, Knierim B, Singh S, Holmes BM, Auer M, Simmons BA, Adams PD, Singh AK. High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresour Technol. 2011 Jan; 102(2):1329-37.
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      105. Chandrasekaran A, Bharadwaj R, Park JI, Sapra R, Adams PD, Singh AK. A microscale platform for integrated cell-free expression and activity screening of cellulases. J Proteome Res. 2010 Nov 5; 9(11):5677-83.
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      106. Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol. 2010; 6(8).
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      107. Liu H, Pereira JH, Adams PD, Sapra R, Simmons BA, Sale KL. Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A. FEBS Lett. 2010 Aug 4; 584(15):3431-5.
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      108. Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons BA, Adams PD. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J Struct Biol. 2010 Dec; 172(3):372-9.
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      109. Pereira JH, Ralston CY, Douglas NR, Meyer D, Knee KM, Goulet DR, King JA, Frydman J, Adams PD. Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J Biol Chem. 2010 Sep 3; 285(36):27958-66.
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      110. Schmidt M, Schwartzberg AM, Carroll A, Chaibang A, Adams PD, Schuck PJ. Raman imaging of cell wall polymers in Arabidopsis thaliana. Biochem Biophys Res Commun. 2010 May 14; 395(4):521-3.
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      111. Nishi K, Lee HJ, Park SY, Bae SJ, Lee SE, Adams PD, Rhee JH, Kim JS. Crystal structure of the transcriptional activator HlyU from Vibrio vulnificus CMCP6. FEBS Lett. 2010 Mar 19; 584(6):1097-102.
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      112. 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. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr. 2010 Feb; 66(Pt 2):213-21.
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      113. Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A. A rapid and inexpensive labeling method for microarray gene expression analysis. BMC Biotechnol. 2009; 9:97.
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      114. Urzhumtsev A, Afonine PV, Adams PD. On the use of logarithmic scales for analysis of diffraction data. Acta Crystallogr D Biol Crystallogr. 2009 Dec; 65(Pt 12):1283-91.
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      115. Moriarty NW, Grosse-Kunstleve RW, Adams PD. electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr D Biol Crystallogr. 2009 Oct; 65(Pt 10):1074-80.
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      116. Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, Terwilliger TC. Recent developments in phasing and structure refinement for macromolecular crystallography. Curr Opin Struct Biol. 2009 Oct; 19(5):566-72.
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      117. Pražnikar J, Afonine PV, Guncar G, Adams PD, Turk D. Averaged kick maps: less noise, more signal... and probably less bias. Acta Crystallogr D Biol Crystallogr. 2009 Sep; 65(Pt 9):921-31.
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      118. Pereira JH, Sapra R, Volponi JV, Kozina CL, Simmons B, Adams PD. Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius. Acta Crystallogr D Biol Crystallogr. 2009 Aug; 65(Pt 8):744-50.
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      119. Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr D Biol Crystallogr. 2009 Jun; 65(Pt 6):582-601.
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      120. Adams PD, Mustyakimov M, Afonine PV, Langan P. Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. Acta Crystallogr D Biol Crystallogr. 2009 Jun; 65(Pt 6):567-73.
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      121. Urzhumtseva L, Afonine PV, Adams PD, Urzhumtsev A. Crystallographic model quality at a glance. Acta Crystallogr D Biol Crystallogr. 2009 Mar; 65(Pt 3):297-300.
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      122. Berman HM, Westbrook JD, Gabanyi MJ, Tao W, Shah R, Kouranov A, Schwede T, Arnold K, Kiefer F, Bordoli L, Kopp J, Podvinec M, Adams PD, Carter LG, Minor W, Nair R, La Baer J. The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res. 2009 Jan; 37(Database issue):D365-8.
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      123. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Adams PD, Read RJ, Zwart PH, Hung LW. Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Crystallogr D Biol Crystallogr. 2008 May; 64(Pt 5):515-24.
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      124. Langan P, Fisher Z, Kovalevsky A, Mustyakimov M, Sutcliffe Valone A, Unkefer C, Waltman MJ, Coates L, Adams PD, Afonine PV, Bennett B, Dealwis C, Schoenborn BP. Protein structures by spallation neutron crystallography. J Synchrotron Radiat. 2008 May; 15(Pt 3):215-8.
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      125. Blanch HW, Adams PD, Andrews-Cramer KM, Frommer WB, Simmons BA, Keasling JD. Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. ACS Chem Biol. 2008 Jan 18; 3(1):17-20.
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      126. Rajalingam D, Kathir KM, Ananthamurthy K, Adams PD, Kumar TK. A method for the prevention of thrombin-induced degradation of recombinant proteins. Anal Biochem. 2008 Apr 15; 375(2):361-3.
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      127. Kim SH, Shin DH, Kim R, Adams P, Chandonia JM. Structural genomics of minimal organisms: pipeline and results. Methods Mol Biol. 2008; 426:475-96.
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      128. Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams PD. Automated structure solution with the PHENIX suite. Methods Mol Biol. 2008; 426:419-35.
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      129. Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD. Surprises and pitfalls arising from (pseudo)symmetry. Acta Crystallogr D Biol Crystallogr. 2008 Jan; 64(Pt 1):99-107.
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      130. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr D Biol Crystallogr. 2008 Jan; 64(Pt 1):61-9.
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      131. Afonine PV, Grosse-Kunstleve RW, Adams PD, Lunin VY, Urzhumtsev A. On macromolecular refinement at subatomic resolution with interatomic scatterers. Acta Crystallogr D Biol Crystallogr. 2007 Nov; 63(Pt 11):1194-7.
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      132. Oganesyan V, Adams PD, Jancarik J, Kim R, Kim SH. Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 May 1; 63(Pt 5):369-74.
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      133. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD, Moriarty NW, Zwart P, Read RJ, Turk D, Hung LW. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Crystallogr D Biol Crystallogr. 2007 May; 63(Pt 5):597-610.
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      134. Terwilliger TC, Adams PD, Moriarty NW, Cohn JD. Ligand identification using electron-density map correlations. Acta Crystallogr D Biol Crystallogr. 2007 Jan; 63(Pt 1):101-7.
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      135. Terwilliger TC, Klei H, Adams PD, Moriarty NW, Cohn JD. Automated ligand fitting by core-fragment fitting and extension into density. Acta Crystallogr D Biol Crystallogr. 2006 Aug; 62(Pt 8):915-22.
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      136. Hohn M, Tang G, Goodyear G, Baldwin PR, Huang Z, Penczek PA, Yang C, Glaeser RM, Adams PD, Ludtke SJ. SPARX, a new environment for Cryo-EM image processing. J Struct Biol. 2007 Jan; 157(1):47-55.
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      137. Adams PD, Oswald RE. Solution structure of an oncogenic mutant of Cdc42Hs. Biochemistry. 2006 Feb 28; 45(8):2577-83.
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      138. Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. Structural basis for double-stranded RNA processing by Dicer. Science. 2006 Jan 13; 311(5758):195-8.
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      139. Xu QS, Jancarik J, Lou Y, Kuznetsova K, Yakunin AF, Yokota H, Adams P, Kim R, Kim SH. Crystal structures of a phosphotransacetylase from Bacillus subtilis and its complex with acetyl phosphate. J Struct Funct Genomics. 2005 Dec; 6(4):269-79.
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      140. Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH. Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP. J Mol Biol. 2005 Nov 25; 354(2):289-303.
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      141. Aishima J, Russel DS, Guibas LJ, Adams PD, Brunger AT. Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface. Acta Crystallogr D Biol Crystallogr. 2005 Oct; 61(Pt 10):1354-63.
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      142. Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams PD, Pace NR. Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13392-7.
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      143. Liu J, Huang C, Shin DH, Yokota H, Jancarik J, Kim JS, Adams PD, Kim R, Kim SH. Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization. J Mol Biol. 2005 Jul 29; 350(5):987-96.
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      144. Oganesyan V, Huang C, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH. Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1; 61(Pt 7):640-6.
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      145. Afonine PV, Grosse-Kunstleve RW, Adams PD. A robust bulk-solvent correction and anisotropic scaling procedure. Acta Crystallogr D Biol Crystallogr. 2005 Jul; 61(Pt 7):850-5.
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      146. Oganesyan V, Oganesyan N, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH. Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus. J Bacteriol. 2005 Jun; 187(12):4238-44.
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      147. Kim JS, DeGiovanni A, Jancarik J, Adams PD, Yokota H, Kim R, Kim SH. Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc Natl Acad Sci U S A. 2005 Mar 1; 102(9):3248-53.
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      148. Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH. Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters. J Biol Chem. 2005 Apr 22; 280(16):15960-6.
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      149. Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim JS, Das D, Schulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, DeGiovanni A, Lou Y, Henriquez M, Huang C, Jancarik J, Pufan R, Choi IG, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams PD, Kim R. Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics. 2005; 6(2-3):63-70.
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      150. Chaudhry C, Horwich AL, Brunger AT, Adams PD. Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. J Mol Biol. 2004 Sep 3; 342(1):229-45.
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      151. Adams PD, Loh AP, Oswald RE. Backbone dynamics of an oncogenic mutant of Cdc42Hs shows increased flexibility at the nucleotide-binding site. Biochemistry. 2004 Aug 10; 43(31):9968-77.
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      152. Kochva U, Leonov H, Arkin IT, Adams PD. Modeling membrane proteins utilizing information from silent amino acid substitutions. Curr Protoc Bioinformatics. 2004 Feb; Chapter 5:Unit5.3.
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      153. Kwon YD, Nagy I, Adams PD, Baumeister W, Jap BK. Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. J Mol Biol. 2004 Jan 2; 335(1):233-45.
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      154. Grosse-Kunstleve RW, Sauter NK, Adams PD. Numerically stable algorithms for the computation of reduced unit cells. Acta Crystallogr A. 2004 Jan; 60(Pt 1):1-6.
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      155. Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC. Recent developments in the PHENIX software for automated crystallographic structure determination. J Synchrotron Radiat. 2004 Jan 1; 11(Pt 1):53-5.
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      156. Grosse-Kunstleve RW, Adams PD. Substructure search procedures for macromolecular structures. Acta Crystallogr D Biol Crystallogr. 2003 Nov; 59(Pt 11):1966-73.
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      157. Grosse-Kunstleve RW, Adams PD. On symmetries of substructures. Acta Crystallogr D Biol Crystallogr. 2003 Nov; 59(Pt 11):1974-7.
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      158. Chaudhry C, Farr GW, Todd MJ, Rye HS, Brunger AT, Adams PD, Horwich AL, Sigler PB. Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. EMBO J. 2003 Oct 1; 22(19):4877-87.
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      159. Pauly TA, Ekstrom JL, Beebe DA, Chrunyk B, Cunningham D, Griffor M, Kamath A, Lee SE, Madura R, Mcguire D, Subashi T, Wasilko D, Watts P, Mylari BL, Oates PJ, Adams PD, Rath VL. X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase. Structure. 2003 Sep; 11(9):1071-85.
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      160. Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR. High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci U S A. 2003 Jun 24; 100(13):7497-502.
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      161. Weeks CM, Adams PD, Berendzen J, Brunger AT, Dodson EJ, Grosse-Kunstleve RW, Schneider TR, Sheldrick GM, Terwilliger TC, Turkenburg MG, Usón I. Automatic solution of heavy-atom substructures. Methods Enzymol. 2003; 374:37-83.
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      162. Adams PD, Grosse-Kunstleve RW, Brunger AT. Computational aspects of high-throughput crystallographic macromolecular structure determination. Methods Biochem Anal. 2003; 44:75-87.
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      163. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr. 2002 Nov; 58(Pt 11):1948-54.
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      164. Adams PD, Chen Y, Ma K, Zagorski MG, Sönnichsen FD, McLaughlin ML, Barkley MD. Intramolecular quenching of tryptophan fluorescence by the peptide bond in cyclic hexapeptides. J Am Chem Soc. 2002 Aug 7; 124(31):9278-86.
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      165. Gottschalk KE, Adams PD, Brunger AT, Kessler H. Transmembrane signal transduction of the alpha(IIb)beta(3) integrin. Protein Sci. 2002 Jul; 11(7):1800-12.
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      166. Brunger AT, Adams PD. Molecular dynamics applied to X-ray structure refinement. Acc Chem Res. 2002 Jun; 35(6):404-12.
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      167. Grosse-Kunstleve RW, Adams PD. Algorithms for deriving crystallographic space-group information. II. Treatment of special positions. Acta Crystallogr A. 2002 Jan; 58(Pt 1):60-5.
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      168. Grosse-Kunstleve RW, Adams PD. Patterson correlation methods: a review of molecular replacement with CNS. Acta Crystallogr D Biol Crystallogr. 2001 Oct; 57(Pt 10):1390-6.
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      169. Adams PD, Grosse-Kunstleve RW. Recent developments in software for the automation of crystallographic macromolecular structure determination. Curr Opin Struct Biol. 2000 Oct; 10(5):564-8.
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