Nigel W Moriarty Publications
2021
- Ibrahim M, Moriarty NW, Kern J, Holton JM, Brewster AS, Bhowmick
A, Bergmann U, Zouni A, Messinger J, Yachandra VK, Yano J, Dobbek H,
Sauter NK, Adams PD:
Reply to Wang et al.: Clear evidence of binding of Ox to the
oxygen-evolving complex of photosystem II is best observed in the omit
map. Proc
Natl Acad Sci U S A. 2021,
118:e2102342118. [PMID: 34117122] [PMCID: PMC8214684]
- van Zundert GCP, Moriarty NW, Sobolev OV, Adams PD, Borrelli KW:
Macromolecular refinement of X-ray and cryoelectron microscopy
structures with Phenix/OPLS3e for improved structure and ligand
quality. Structure
2021,
[epub ahead of print] [PMID: 33823127] [PMCID: ]
- Liebschner D, Afonine PV, Moriarty NW, Poon BK, Chen VB, Adams PD:
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. Acta Cryst.
2021,
D77:48-61. [PMID: 33404525] [PMCID: PMC7787109]
2020
-
Wang L,
Kruse H,
Sobolev OV,
Moriarty NW,
Waller MP,
Afonine PV,
Biczysko M:
Real-space quantum-based refinement for cryo-EM: Q|R#3.
Acta Cryst.
2020,
76:1184-1191
- Moriarty NW, Liebschner D, Tronrud DE, Adams PD:
Arginine off-kilter: guanidinium is not as planar as restraints denote. Acta Cryst.
2020,
D76:1159-1166. [PMID: 33263321] [PMCID: PMC7709202]
- Sobolev OV, Afonine PV, Moriarty NW, Hekkelman ML, Joosten RP, Perrakis A, Adams PD:
A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. Structure
2020,
28:1249-1258.e2. [PMID: 32857966] [PMCID: PMC7642142]
- Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle
L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de
Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N,
Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S,
Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H,
Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J,
Kern J, Yachandra VK, Yano J:
Untangling the sequence of events during the S2 ➔
S3 transition in photosystem II and implications for the
water oxidation mechanism. Proc Natl Acad Sci
U S A. 2020,
117:12624-12635. [PMID: 32434915] [PMCID: PMC7293653]
- Liebschner D, Afonine PV, Moriarty NW, Adams PD:
What Are the Current Limits on Determination of Protonation State
Using Neutron Macromolecular Crystallography? Methods
Enzymol. 2020,
634:225-255 [PMID: 32093835] [PMCID: PMC7571246]
-
Moriarty NW,
Janowski PA,
Swails JM,
Nguyen H,
Richardson JS,
Case DA,
Adams PD:
Improved chemistry restraints for crystallographic refinement by
integrating the Amber force field into Phenix.
Acta Cryst.
2020,
76:51-62
-
Zheng M,
Biczysko M,
Xu Y,
Moriarty NW,
Kruse H,
Urzhumtsev A,
Waller MP,
Afonine PV:
Including crystallographic symmetry in quantum-based refinement: Q|R#2.
Acta Cryst.
2020,
76:41-50 [PMID: 31909743] [PMCID: PMC6939439]
2019
- Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI,
Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK,
Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev
OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams
CJ, Adams PD:
Macromolecular structure determination using X-rays, neutrons and
electrons: recent developments in Phenix. Acta Cryst.
2019,
75:861-877 [PMID: 31588918] [PMCID: PMC6778852 ]
- Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev
OV, Adams PD, Sanbonmatsu K:
Cryo_fit: Democratization of flexible fitting for cryo-EM. J Struct Biol. 2019,
208:1-6 [PMID: 31279069] [PMCID: ]
- Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J,
Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas
A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y,
Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M,
Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S,
Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY:
Announcing mandatory submission of PDBx/mmCIF format files for
crystallographic depositions to the Protein Data Bank (PDB). Acta Cryst.
2019,
D75:451-454. [PMID: 30988261] [PMCID: PMC6465986]
- Moriarty NW, Adams PD:
Iron-sulfur clusters have no right angles. Acta Cryst.
2019,
D75:16-20. [PMID: 30644841] [PMCID: PMC6333285]
2018
- Jiang ZM, Biczysko M, Moriarty NW:
Accurate geometries for "Mountain pass" regions of the Ramachandran plot using quantum chemical calculations.
Proteins: Struct, Funct, Bioinf.
86:273-278
- Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA,
Moriarty NW, 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. Cryst.
2018, 51:193-199 [PMID: 29507550] [PMCID: PMC5822993]
- Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis
LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall
WB 3rd, 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,
27:293-315 [PMID: 29067766] [PMCID: PMC5734394]
- Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd J, Poon BK, Adams PD:
Interactive Comparison and Remediation of Collections of Macromolecular Structures. Protein Sci. 2018,
27:182-194 [PMID: 28901593] [PMCID: PMC5734393]
2017
- Zheng M, Moriarty NW, Xu YT, Reimers JR, Afonine PV, Waller MP:
Solving the scalability issue in quantum-based refinement: Q|R#1.
Acta Cryst. 2017,
D73:1020-1028
- Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD:
Polder maps: improving OMIT maps by excluding bulk solvent. Acta Cryst. 2017,
D73:148-157 [PMID: 28177311] [PMCID: PMC5297918]
- Moriarty NW, Draizen EJ, Adams PD:
An editor for the generation and customization of geometry restraints. Acta Cryst. 2017,
D73:123-130 [PMID: 28177308] [PMCID: PMC5297915]
2016
- Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller FD, 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, Vo Pham L, 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 NW, 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, 540:453-457 [PMID: 27871088] [PMCID: PMC5201176]
- Janowski PA, Moriarty NW, Kelley BP, Case DA, York DM, Adams PD, Warren GL:
Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Cryst.
2016, D72:1062-7 [PMID: 27599738] [PMCID: PMC5013598]
- Moriarty NW, Tronrud DE, Adams PD, Karplus PA:
A new default restraint library for the protein backbone in Phenix:
a conformation-dependent geometry goes mainstream Acta Cryst.
2016, 72:176-179 [PMID: 26894545] [PMCID: PMC4756615]
2015
- Hill, CH, Viuff, AH, Spratley, SJ, Salamone, S, Christensen, SH,
Read, RJ, Moriarty, NW, Jensen, HH, Deane, JE:
Azasugar inhibitors as pharmacological chaperones for Krabbe disease.
Chemical Science 2015, 6:3075-3086.
- Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger
TC, Turk D, Urzhumtsev A, Adams PD: FEM: feature-enhanced map.
Acta
Cryst. 2015, D71:646-666. [PMID: 25760612] [PMCID: PMC4356370]
2014
- 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.
2014,9:2286-93. [PMID: 25047814] [PMCID: PMC4213943]
- Moriarty NW, Tronrud DE, Adams PD, Karplus PA:
Conformation-dependent backbone geometry restraints set a new
standard for protein crystallographic refinement. FEBS J. 2014,
281:4061-71. [PMID: 24890778] [PMCID: PMC4169323]
- Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD:
Flexible torsion-angle noncrystallographic symmetry restraints for
improved macromolecular structure refinement. Acta Cryst.
2014, D70:1346-1356. [PMID: 24816103] [PMCID: PMC4014122]
- 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 Cryst.
2014, D70:144-154. [PMID: 24419387] [PMCID: PMC3919266]
- 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 Cryst.
2014, D70:134-143. [PMID: 24419386] [PMCID: PMC3919265]
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.
J. Appl. Cryst. 2012, 45:581-586 [PMID: 22675231] [PMCID: PMC3359726]
- 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 [PMID: 22505256] [PMCID: PMC3322595]
- 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 [PMID: 22505258] [PMCID: PMC3322597]
2011
- Adams PD, Afonine PV, Bunkóczi 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.
In International Tables for Crystallography, Volume F:
Crystallography of Biological Macromolecules, E. Arnold, D.M
Himmel and M.G. Rossmann, Eds, John Wiley and Sons, Ltd,
2011, 539-547.
- 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, 55:94-106 [PMID: 21821126] [PMCID: PMC3193589]
2010
- Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty
NW, Langan P, Adams PD:
Joint X-ray and neutron refinement with phenix.refine.
Acta Cryst. 2010, D66:1153-1163. [PMID: 21041930] [PMCID: PMC2967420]
- Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, 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. Cryst. 2010, 43:677-685. [PMID: 20648263] [PMCID: PMC2906258]
- Adams PD, Afonine PV, Bunkóczi 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.
2009
- Moriarty NW, Grosse-Kunstleve RW, Adams PD:
electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation.
Acta Cryst. 2009, D65:1074-1080.
- Grosse-Kunstleve RW, Moriarty NW, Adams PD:
Torsion Angle Refinement and Dynamics as a tool to aid crystallographic Structure Determination.
Proceedings of ASME 2009 International Design Engineering Technical Conferences, San Diego, California 2009, August 30 - September 2. Paper #DETC2009-87737. ASME Press.
- Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung L-W:
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.
Acta Cryst. 2009, D65:582-601.
2008
- 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 Cryst. 2008, D64:515-524.
- Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung L-W, 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 in Molecular Biology 2008, 426:419-435.
- 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 Cryst. 2008, D64:61-69.
2007
-
Adams PD, Afonine, PV, Grosse-Kunstleve RW, Moriarty NW, Sauter NK,
Zwart PH, Gopal K, Ioerger TR, Kanbi L, McKee E, Pai RK, Hung L-W,
Radhakannan T, McCoy AJ, Read RJ, Storoni LC, Romo TD, Sacchettini JC,
Terwilliger TC: Automated structure determination with Phenix.
In Evolving Methods for Macromolecular Crystallography. Read RJ
and Sussman JL, Eds, Springer, Dordrecht, The Netherlands. 2007,
101-109.
-
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 Cryst. 2007, D63:597-610.
-
Terwilliger TC, Adams PD, Moriarty NW, Cohn JD:
Ligand identification using electron-density map correlations.
Acta Cryst. 2007, D63:101-107.
2006
-
Terwilliger TC, Klei H, Adams PD, Moriarty NW, Cohn JD:
Automated ligand fitting by core-fragment fitting and extension into density.
Acta Cryst. D62, 915-922.
2004
- Adams PD, Gopal K, Grosse-Kunstleve RW, Hung L-W, 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 Rad. 2004, 11:53-55.
2003
2002
- Adams PD, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ,
Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC:
PHENIX: building new software for automated crystallographic
structure determination Acta Cryst.
2002, D58:1948-1954.
- Grosse-Kunstleve RW, Sauter NK, Moriarty NW, Adams PD: The
Computational Crystallography Toolbox: crystallographic algorithms in
a reusable software framework
J. Appl. Cryst. 2002, 35:126-136.
2001
2000
-
Nigel W. Moriarty and Michael Frenklach.
Ab initio study of napthalene formation by addition of
vinylacetylene to phenyl.
Proceedings of the Combustion Institute
2000, 28:2563-2568.
-
Hai Wang,
Alexander Laskin, Nigel W. Moriarty and Michael Frenklach.
On unimolecular decomposition of phenyl radical.
Proceedings of the Combustion Institute
2000, 28:1545-1555.
1999
-
Xénophon Krokidis, Nigel W. Moriarty, William A. Lester Jr.
and Michael Frenklach.
Progargyl: An electron localization function study.
Chemical Physics Letters
1999, 314:541-549.
-
Nigel W. Moriarty, Nancy J. Brown and Michael Frenklach.
Hydrogen migration in the phenylethen-2-yl radical.
Journal of Physical Chemistry A.
1999, 103:7127-7135.
-
Shaheen R. Tonse, Nigel W. Moriarty, Nancy J. Brown and Michael Frenklach.
PRISM: Piecewise Reusable Implementation of Solution Mapping.
An economical strategy for chemical kinetics.
Israel Journal of Chemistry
1999, 39:97-106.
1998
-
Michael Frenklach, Nigel W. Moriarty and Nancy J. Brown.
Hydrogen migration in polyaromatic growth.
Proceedings of the Combustion Institute
1998, 27:1655-1661.
-
Nigel W. Moriarty, Roland Lindh and Gunnar Karlström.
Tetramethylene: A CASPT2 study.
Chemical Physics Letters
1998, 289:442-450.
1997
-
Nigel W. Moriarty and Gunnar Karlström.
Electric field gradients of water in water.
A combined quantum chemical and statistical mechanical treatment.
Chemical Physics Letters
1997 279:372-376.
-
Nigel W. Moriarty and Gunnar Karlström.
Geometry optimization of a water molecule in water.
A combined quantum chemical and statistical mechanical treatment.
Journal of Chemical Physics
1997, 106:6470-6474.
1996
-
Nigel W. Moriarty and Gunnar Karlström.
Electronic polarization of a water molecule in water.
A combined quantum chemical and statistical mechanical treatment.
Journal of Physical Chemistry
1996 100:17791-17796.
-
Eric Magnusson and Nigel W. Moriarty.
Binding patterns in single-ligand complexes of NH3,
H2O, OH-, and F- with first
series transition metals.
Inorganic Chemistry
1996 35:5711-5719.
1993
-
Eric Magnusson and Nigel W. Moriarty.
Computational convergence of electronic structure calculations of
transition metal ligand complexes.
Journal of Computational Chemistry
1993 14:961-969.
1992
-
Nigel W. Moriarty and Philip V. Smith.
The chemisorption of NH3 on the Si(100) surface.
Surface Science
1992 265:168-174.
