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Moriarty, Nigel

TitleComputer Scientist
InstitutionLawrence Berkeley National Lab
DepartmentMolecular Biophys & Integ Bio
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/486-5709
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty N, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM. DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs. J Appl Crystallogr. 2018 Feb 01; 51(Pt 1):193-199. PMID: 29507550.
      View in: PubMed
    2. Jiang Z, Biczysko M, Moriarty N. Accurate geometries for "Mountain pass" regions of the Ramachandran plot using quantum chemical calculations. Proteins. 2018 Mar; 86(3):273-278. PMID: 29314245.
      View in: PubMed
    3. Zheng M, Moriarty N, Xu Y, Reimers JR, Afonine PV, Waller MP. Solving the scalability issue in quantum-based refinement: Q|R#1. Acta Crystallogr D Struct Biol. 2017 Dec 01; 73(Pt 12):1020-1028. PMID: 29199981.
      View in: PubMed
    4. Williams CJ, Headd JJ, Moriarty N, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018 Jan; 27(1):293-315. PMID: 29067766.
      View in: PubMed
    5. Moriarty N, Liebschner D, Klei HE, Echols N, Afonine PV, Headd JJ, Poon BK, Adams PD. Interactive comparison and remediation of collections of macromolecular structures. Protein Sci. 2018 Jan; 27(1):182-194. PMID: 28901593.
      View in: PubMed
    6. Liebschner D, Afonine PV, Moriarty N, Poon BK, Sobolev OV, Terwilliger TC, Adams PD. Polder maps: improving OMIT maps by excluding bulk solvent. Acta Crystallogr D Struct Biol. 2017 Feb 01; 73(Pt 2):148-157. PMID: 28177311.
      View in: PubMed
    7. Moriarty N, Draizen EJ, Adams PD. An editor for the generation and customization of geometry restraints. Acta Crystallogr D Struct Biol. 2017 Feb 01; 73(Pt 2):123-130. PMID: 28177308.
      View in: PubMed
    8. Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty N, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J. Structure of photosystem II and substrate binding at room temperature. Nature. 2016 12 15; 540(7633):453-457. PMID: 27871088.
      View in: PubMed
    9. Janowski PA, Moriarty N, Kelley BP, Case DA, York DM, Adams PD, Warren GL. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Crystallogr D Struct Biol. 2016 09; 72(Pt 9):1062-72. PMID: 27599738.
      View in: PubMed
    10. Moriarty N, Tronrud DE, Adams PD, Karplus PA. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. Acta Crystallogr D Struct Biol. 2016 Jan; 72(Pt 1):176-9. PMID: 26894545; PMCID: PMC4756615.
    11. Hill CH, Viuff AH, Spratley SJ, Salamone S, Christensen SH, Read RJ, Moriarty N, Jensen HH, Deane JE. Azasugar inhibitors as pharmacological chaperones for Krabbe disease. Chem Sci. 2015 May 20; 6(5):3075-3086. PMID: 26029356.
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    12. Afonine PV, Moriarty N, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD. FEM: feature-enhanced map. Acta Crystallogr D Biol Crystallogr. 2015 Mar; 71(Pt 3):646-66. PMID: 25760612; PMCID: PMC4356370.
    13. Pereira JH, Petchprayoon C, Hoepker AC, Moriarty N, 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. PMID: 25047814; PMCID: PMC4213943.
    14. Moriarty N, 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. PMID: 24890778; PMCID: PMC4169323.
    15. Headd JJ, Echols N, Afonine PV, Moriarty N, 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. PMID: 24816103; PMCID: PMC4014122.
    16. Echols N, Moriarty N, 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. PMID: 24419387.
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    17. Klei HE, Moriarty N, 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. PMID: 24419386; PMCID: PMC3919265.
    18. Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, McCoy AJ, Moriarty N, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams PD. Graphical tools for macromolecular crystallography in PHENIX. J Appl Crystallogr. 2012 Jun 01; 45(Pt 3):581-586. PMID: 22675231.
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    19. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty N, 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. PMID: 22505256; PMCID: PMC3322595.
    20. Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty N, 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. PMID: 22505258; PMCID: PMC3322597.
    21. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty N, 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. PMID: 21821126.
      View in: PubMed
    22. Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty N, 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. PMID: 21041930; PMCID: PMC2967420.
    23. Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty N, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J Appl Crystallogr. 2010 Aug 01; 43(Pt 4):669-676. PMID: 20648263.
      View in: PubMed
    24. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty N, 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. PMID: 20124702.
      View in: PubMed
    25. Moriarty N, 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. PMID: 19770504; PMCID: PMC2748967.
    26. Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty N, 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. PMID: 19465773.
      View in: PubMed
    27. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty N, 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. PMID: 18453687; PMCID: PMC2424225.
    28. Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty N, 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. PMID: 18542881.
      View in: PubMed
    29. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty N, 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. PMID: 18094468; PMCID: PMC2394820.
    30. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD, Moriarty N, 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. PMID: 17452785; PMCID: PMC2483474.
    31. Terwilliger TC, Adams PD, Moriarty N, Cohn JD. Ligand identification using electron-density map correlations. Acta Crystallogr D Biol Crystallogr. 2007 Jan; 63(Pt 1):101-7. PMID: 17164532; PMCID: PMC2483487.
    32. Terwilliger TC, Klei H, Adams PD, Moriarty N, 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. PMID: 16855309; PMCID: PMC2745883.
    33. Adams PD, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty N, 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 01; 11(Pt 1):53-5. PMID: 14646133.
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    34. Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty N, 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. PMID: 12393927.
      View in: PubMed
    35. Magnusson E, Moriarty N. Binding Patterns in Single-Ligand Complexes of NH(3), H(2)O, OH(-), and F(-) with First Series Transition Metals. Inorg Chem. 1996 Sep 11; 35(19):5711-5719. PMID: 11666766.
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