journal {
  name = Acta Cryst. D
  name = Acta Crystallogr D Biol Crystallogr
  name_full = Acta Crystallographica, Section D: Biological Crystallography
  abbrev_CAS = Acta Crystallogr., Sect. D: Biol. Crystallogr.
  id_ASTM = ABCRE6
  id_ISSN = 0907-4449
  id_CSD = 0766
}

journal {
  name = Nature
  name_full = Nature (London, United Kingdom)
  abbrev_CAS = Nature (London, U. K.)
  id_ASTM = NATUAS
  id_ISSN = None
  id_CSD = 0006
}

journal {
  name = J. Mol. Biol.
  name_full = Journal of Molecular Biology
  abbrev_CAS = J. Mol. Biol.
  id_ASTM = JMOBAK
  id_ISSN = None
  id_CSD = 0070
}

journal {
  name = J. Synchrotron Rad.
  name_full = Journal of Synchrotron Radiation
  abbrev_CAS = J. Synchrotron Rad.
  id_ASTM = JSYRES
  id_ISSN = None
  id_CSD = 1210
}

journal {
  name = J. Appl. Cryst.
  name = J Appl Crystallogr
  name_full = Journal of Applied Crystallography
  abbrev_CAS = J. Appl. Crystallogr.
  id_ASTM = JACGAR
  id_ISSN = None
  id_CSD = 0228
}

journal {
  name = J. Comput. Chem.
  name_full = Journal of Computational Chemistry
  abbrev_CAS = J. Comput. Chem.
  id_ASTM = JCCHDD
  id_ISSN = None
  id_CSD = 0913
}

journal {
  name = Biopolymers
  abbrev_CAS = Biopolymers
  id_ASTM = BIPMAA
  id_ISSN = None
  id_CSD = 0161
}

journal {
  name = Nucleic Acids Research
  name_full = Nucleic Acids Research
  abbrev_CAS = Nucleic Acids Res.
  id_ASTM = NARHAD
  id_ISSN = None
  id_CSD = 0389
}

journal {
  name = Science
  name_full = Science (Washington, DC, United States)
  abbrev_CAS = Science (Washington, DC, U. S.)
  id_ASTM = SCIEAS
  id_ISSN = None
  id_CSD = 0038
}

journal {
  name = eLife
  abbrev_CAS = eLife
  id_ASTM = None
  id_ISSN = None
  id_CSD = None
}

journal {
  name = Computational Crystallography Newsletter
  abbrev_CAS = Comput. Cryst. Newsl.
  id_ASTM = None
  id_ISSN = None
  id_CSD = None
}

journal {
  name = Protein Science
  name_full = Protein Science
  abbrev_CAS = Protein Sci.
  id_ASTM = PRCIEI
  id_ISSN = 1469-896X
  id_CSD = None
}

citation {
  article_id = hhpred
  authors = Söding J
  title = Protein homology detection by HMM-HMM comparison.
  journal = Bioinformatics
  volume = 21
  pages = 951-60
  year = 2005
  doi_id = "10.1093/bioinformatics/bti125"
  pmid = 15531603
  external = True
}

citation {
  article_id = erraser
  authors = Chou FC, Sripakdeevong P, Dibrov SM, Hermann T, Das R
  title = Correcting pervasive errors in RNA crystallography through enumerative structure prediction.
  journal = Nat Methods
  volume = 10
  pages = 74-6
  year = 2012
  doi_id = "10.1038/nmeth.2262"
  pmid = 23202432
  external = True
}

citation {
  article_id = rosetta_phaser
  authors = Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D
  title = High-resolution structure prediction and the crystallographic phase problem.
  journal = Nature
  volume = 450
  pages = 259-64
  year = 2007
  doi_id = "10.1038/nature06249"
  pmid = 17934447
}

citation {
  article_id = mr_rosetta
  authors = DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D
  title = Improved molecular replacement by density- and energy-guided protein structure optimization.
  journal = Nature
  volume = 473
  pages = 540-3
  year = 2011
  doi_id = "10.1038/nature09964"
  pmid = 21532589
}

citation {
  article_id = mr_rosetta_icsg
  authors = Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N
  title = phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.
  journal = J Struct Funct Genomics
  volume = 13
  pages = 81-90
  year = 2012
  doi_id = "10.1007/s10969-012-9129-3"
  pmid = 22418934
}

citation {
  article_id = seq_assign
  authors = Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Hung LW
  title = Model morphing and sequence assignment after molecular replacement.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 69
  pages = 2244-50
  year = 2013
  doi_id = "10.1107/S0907444913017770"
  pmid = 24189236
}

citation {
  article_id = morph_model
  authors = Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Grosse-Kunstleve RW, Hung LW
  title = Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 68
  pages = 861-70
  year = 2012
  doi_id = "10.1107/S0907444912015636"
  pmid = 22751672
}


citation {
  article_id = rosetta_density
  authors = DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D
  title = Refinement of protein structures into low-resolution density maps using rosetta.
  journal = J Mol Biol
  volume = 392
  pages = 181-90
  year = 2009
  doi_id = "10.1016/j.jmb.2009.07.008"
  pmid = 19596339
  external = True
}

citation {
  article_id = autobuild
  authors = Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, \
    Zwart PH, Hung L-W, Read RJ, Adams PD
  title = Iterative model building, structure refinement and density \
    modification with the PHENIX AutoBuild wizard
  year = 2008
  journal = Acta Cryst. D
  volume = 64
  pages = 61-69
  pmid = 18094468
  doi_id = doi:10.1107/S090744490705024X
}

citation {
  article_id = resolve_model_build
  authors = Terwilliger TC
  title = Automated main-chain model building by template matching and iterative fragment extension.
  year = 2003
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 59
  pages = 38-44
  pmid = 12499537
  doi_id = doi:10.1107/S0907444902018036
}

citation {
  article_id = resolve_seq_assign
  authors = Terwilliger TC
  title = Automated side-chain model building and sequence assignment by template matching.
  year = 2003
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 59
  pages = 45-9
  pmid = 12499538
  doi_id = doi:10.1107/S0907444902018048
}

citation {
  article_id = dm_pattern
  authors = Terwilliger TC
  title = Statistical density modification using local pattern matching.
  year = 2003
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 59
  pages = 1688-701
  pmid = 14501107
  doi_id = doi:10.1107/S0907444903015142
}

citation {
  article_id = iterative_build
  authors = Terwilliger TC
  title = Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement.
  year = 2003
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 59
  pages = 1174-82
  pmid = 12832760
  doi_id = doi:10.1107/S0907444903009922
}

citation {
  article_id = protein_ligand_pipeline
  authors = Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD
  title = Automating crystallographic structure solution and refinement of protein-ligand complexes.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 70
  pages = 144-54
  year = 2014
  doi_id = "10.1107/S139900471302748X"
  pmid = 24419387
}


citation {
  article_id = glr
  authors = Klei HE, Moriarty NW, Echols N, Terwilliger TC, Baldwin ET, Pokross M, Posy S, Adams PD
  title = Ligand placement based on prior structures: the guided ligand-replacement method.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 70
  pages = 134-43
  year = 2014
  doi_id = "10.1107/S1399004713030071"
  pmid = 24419386
}
citation {
  article_id = ligand_fit
  authors = Terwilliger TC, Klei H, Adams PD, Moriarty NW, Cohn JD
  title = Automated ligand fitting by core-fragment fitting and extension into density.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 62
  pages = 915-22
  year = 2006
  doi_id = "10.1107/S0907444906017161"
  pmid = 16855309
}

citation {
  article_id = ligand_id
  authors = Terwilliger TC, Adams PD, Moriarty NW, Cohn JD
  title = Ligand identification using electron-density map correlations.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 63
  pages = 101-7
  year = 2006
  doi_id = "10.1107/S0907444906046233"
  pmid = 17164532
}

citation {
  article_id = autobuild_omit
  authors = Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, \
    Adams PD, Read RJ, Zwart PH, Hung L-W
  title = Iterative-build OMIT maps: map improvement by iterative model \
    building and refinement without model bias.
  year = 2008
  journal = Acta Cryst. D
  volume = 64
  pages = 515-524
  pmid = 18453687
  doi_id =  doi:10.1107/S0907444908004319
}

citation {
  article_id = autobuild_mult
  authors = Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, \
    Adams PD, Moriarty NW, \
    Zwart PH, Read RJ, Turk D, Hung L-W
  title = Interpretation of ensembles created by multiple iterative \
      rebuilding of macromolecular models
  year = 2007
  journal = Acta Cryst. D
  volume = 63
  pages = 597-610
  pmid = 17452785
  doi_id = doi:10.1107/S0907444907009791
}

citation {
  article_id = solve_resolve
  authors = Terwilliger T
  title = SOLVE and RESOLVE: automated structure solution, density modification and model building.
  journal = J Synchrotron Radiat
  volume = 11
  pages = 49-52
  year = 2003
  doi_id =  doi:10.1107/S0909049503023938
  pmid = 14646132
}

citation {
  article_id = merritt_server
  authors = Merritt EA
  title = X-ray Anomalous Scattering
  year = 2012
  journal = http://www.bmsc.washington.edu/scatter
  volume = None
  pages = None
  external = True
}

citation {
  article_id = autosol
  authors = Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW
  title = Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.
  journal = Acta Crystallogr D Biol Crystallogr
  year = 2009
  volume = 65
  pages = 582-601
  doi_id = "10.1107/S0907444909012098"
  pmid = 19465773
}

citation {
  article_id = elbow
  authors = Moriarty NW, Grosse-Kunstleve RW, Adams PD
  title = electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 65
  pages = 1074-80
  year = 2009
  doi_id = "10.1107/S0907444909029436"
  pmid = 19770504
}

citation {
  article_id = reel
  authors = Moriarty NW, Draizen EJ, Adams PD
  title = An editor for the generation and customization of geometry restraints
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 73
  pages = 123-130
  year = 2017
  doi_id = "10.1107/S2059798316016570"
  pmid = 28177308
}

citation {
  article_id = find_ncs
  authors = Terwilliger TC
  title = Rapid automatic NCS identification using heavy-atom substructures.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 58
  pages = 2213-5
  year = 2002
  doi_id =  doi:10.1107/S0907444902016384
  pmid = 12454504
}

citation {
  article_id = prime_and_switch
  authors = Terwilliger TC
  title = Using prime-and-switch phasing to reduce model bias in molecular replacement.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 60
  pages = 2144-9
  year = 2004
  doi_id = "10.1107/S0907444904019535"
  pmid = 15572767
}


citation {
  article_id = bayes_fa
  authors = Terwilliger TC
  title = MAD phasing: Bayesian estimates of F(A).
  journal = Acta Crystallogr D Biol Crystallogr
  year = 1994
  volume = 50
  pages = 11-6
  doi_id = "10.1107/S0907444993008224"
  pmid = 15299471
}

citation {
  article_id = resolve_oasis
  authors = Wang JW, Chen JR, Gu YX, Zheng CD, Jiang F, Fan HF, Terwilliger TC, Hao Q
  title = SAD phasing by combination of direct methods with the SOLVE/RESOLVE procedure.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 60
  pages = 1244-53
  year = 2004
  doi_id = "10.1107/S0907444904010674"
  pmid = 15213386
}

citation {
  article_id = bss
  authors = Afonine PV, Grosse-Kunstleve RW, Adams PD
  title = A robust bulk-solvent correction and anisotropic scaling procedure.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 61
  pages = 850-5
  year = 2005
  doi_id = "10.1107/S0907444905007894"
  pmid = 15983406
}

citation {
  article_id = cctbx
  authors = Grosse-Kunstleve RW, Sauter NK, Moriarty NW, Adams PD
  title = The Computational Crystallography Toolbox: crystallographic \
    algorithms in a reusable software framework
  year = 2002
  journal = J. Appl. Cryst.
  volume = 35
  pages = 126-136
  doi_id = doi:10.1107/S0021889801017824
}

citation {
  article_id = hyss
  authors = Grosse-Kunstleve RW, Adams PD
  title = Substructure search procedures for macromolecular structures
  year = 2003
  journal = Acta Cryst. D
  volume = 59
  pages = 1966-1973.
  doi_id = doi:10.1107/S0907444903018043
}

citation {
  article_id = ias
  authors = Afonine PV, Grosse-Kunstleve RW, Adams PD, Lunin VY, \
    Urzhumtsev A
  title = On macromolecular refinement at subatomic resolution with \
    interatomic scatterers
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 63
  pages = 1194-7
  year = 2007
  doi_id = "10.1107/S0907444907046148"
  pmid = 18007035
}

citation {
  article_id = kicked_maps
  authors = Pražnikar J, Afonine PV, Guncar G, Adams PD, Turk D
  title = Averaged kick maps: less noise, more signal... and probably less bias.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 65
  pages = 921-31
  year = 2009
  doi_id = "10.1107/S0907444909021933"
  pmid = 19690370
}

citation {
  article_id = molprobity
  authors = Williams CJ, Hintze BJ, Headd JJ, Moriarty NW, Chen VB, Jain S, \
    Prisant MG Lewis SM, Videau LL, Keedy DA, Deis LN, Arendall WB III, \
    Verma V, Snoeyink JS, Adams PD, Lovell SC, Richardson JS, Richardson DC
  title = MolProbity: More and better reference data for improved all-atom \
    structure validation
  year = 2018
  journal = Protein Science
  volume = 27
  pages = 293-315
  doi_id =  doi:10.1002/pro.3330
}

citation {
  article_id = phaser
  authors = McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ
  title = Phaser crystallographic software.
  journal = J Appl Crystallogr
  volume = 40
  pages = 658-674
  year = 2007
  doi_id = "10.1107/S0021889807021206"
  pmid = 19461840
}

citation {
  article_id = sad_function
  authors = McCoy AJ, Storoni LC, Read RJ
  title = Simple algorithm for a maximum-likelihood SAD function.
  journal = Acta Crystallogr D Biol Crystallogr
  year = 2004
  volume = 60
  pages = 1220-8
  doi_id = "10.1107/S0907444904009990"
  pmid = 15213383
}

citation {
  article_id = phenix2002
  authors = Adams PD, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC
  title = PHENIX: building new software for automated crystallographic structure determination.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 58
  pages = 1948-54
  year = 2002
  doi_id = doi:10.1107/S0907444902016657
  pmid = 12393927
}

citation {
  article_id = phenix2010
  authors = Adams PD, Afonine PV, Bunkoczi 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
  title = PHENIX: a comprehensive Python-based system for macromolecular structure solution
  year = 2010
  journal = Acta Cryst. D
  volume = 66
  pages = 213-221
  pmid = 20124702
  doi_id = "10.1107/S0907444909052925"
}

citation {
  article_id = phenix
  authors = 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
  title = Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
  year = 2019
  journal = Acta Cryst. D
  volume = 75
  pages = 861-877
  doi_id = "10.1107/S2059798319011471"
}

citation {
  article_id = phenix.refine
  authors = Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD
  title = Towards automated crystallographic structure refinement with phenix.refine.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 68
  pages = 352-67
  year = 2012
  doi_id = "10.1107/S0907444912001308"
  pmid = 22505256
}

citation {
  article_id = polygon
  authors = Urzhumtseva L, Afonine PV, Adams PD, Urzhumtsev A
  title = Crystallographic model quality at a glance
  year = 2009
  journal = Acta Cryst. D
  volume = 65
  pages = 297-300
  pmid = 19237753
  doi_id = doi:10.1107/S0907444908044296
}

citation {
  article_id = pulchra
  authors = Rotkiewicz P, Skolnick J
  title = Fast procedure for reconstruction of full-atom protein models from reduced representations.
  journal = J Comput Chem
  volume = 29
  pages = 1460-5
  year = 2008
  doi_id = "10.1002/jcc.20906"
  pmid = 18196502
  external = True
}

citation {
  article_id = rigid_body
  authors = Afonine PV, Grosse-Kunstleve RW, Urzhumtsev A, Adams PD
  title = Automatic multiple-zone rigid-body refinement with a large convergence radius.
  journal = J Appl Crystallogr
  volume = 42
  pages = 607-615
  year = 2009
  doi_id = "10.1107/S0021889809023528"
  pmid = 19649324
}


citation {
  article_id = buccaneer
  authors = Cowtan K
  title = The Buccaneer software for automated model building. 1. Tracing protein chains.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 62
  pages = 1002-11
  year = 2006
  doi_id = "10.1107/S0907444906022116"
  pmid = 16929101
  external = True
}


citation {
  article_id = xtriage
  authors = Zwart PH, Grosse-Kunstleve RW, Adams PD
  title =  Xtriage and Fest: automatic assessment of X-ray data and \
    substructure structure factor estimation
  year = 2005
  journal = CCP4 Newsletter
  volume = Winter
  pages = Contribution 7
}

citation {
  article_id = ksdssp
  authors = Kabsch W, Sander C
  title = Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
  journal = Biopolymers
  volume = 22
  pages = 2577-637
  year = 1984
  doi_id = "10.1002/bip.360221211"
  pmid = 6667333
  external = True
}

citation {
  article_id = muscle
  authors = Edgar RC
  title = MUSCLE: multiple sequence alignment with high accuracy and high throughput.
  journal = Nucleic Acids Res
  volume = 32
  pages = 1792-7
  year = 2004
  doi_id = "10.1093/nar/gkh340"
  pmid = 15034147
  external = True
}


citation {
  article_id = reference_model
  authors = Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD
  title = Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution
  year = 2012
  journal = Acta Cryst. D
  volume = 68
  pages = 381-390
  doi_id = "10.1107/S0907444911047834"
}

citation {
  article_id = den_refine
  authors = Schröder GF, Levitt M, Brunger AT
  title = Super-resolution biomolecular crystallography with low-resolution data.
  journal = Nature
  volume = 464
  pages = 1218-22
  year = 2010
  doi_id = "10.1038/nature08892"
  pmid = 20376006
  external = True
}

citation {
  article_id = phenix_gui
  authors = 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
  title = Graphical tools for macromolecular crystallography in PHENIX.
  year = 2012
  journal = J. Appl. Cryst.
  volume = 45
  pages = 581-586
  doi_id = "10.1107/S0021889812017293"
}

citation {
  article_id = cc_star
  authors = Karplus PA, Diederichs K
  title = Linking crystallographic model and data quality.
  year = 2012
  journal = Science
  volume = 336
  pages = 1030-1033
  doi_id = "10.1126/science.1218231"
}

citation {
  article_id = ensemble_refinement
  authors = Burnley BT, Afonine PV, Adams PD, Gros P.
  title = Modelling dynamics in protein crystal structures by ensemble refinement.
  year = 2012
  journal = eLife
  volume = 1
  doi_id = "10.7554/eLife.00311"
}

citation {
  article_id = coot
  authors = Emsley P, Lohkamp B, Scott WG, Cowtan K.
  title = Features and development of Coot.
  year = 2010
  journal = Acta Cryst. D
  volume = 66
  pages = 486-501
  doi_id = "10.1107/S0907444910007493"
}

citation {
  article_id = rosetta_refine
  authors = DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D
  title = Improved low-resolution crystallographic refinement with Phenix and Rosetta.
  journal = Nat Methods
  volume = 10
  pages = 1102-4
  year = 2013
  doi_id = "10.1038/nmeth.2648"
  pmid = 24076763
}

citation {
  article_id = rosetta_scripts
  authors = Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D
  title = RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite.
  journal = PLoS One
  volume = 6
  pages = e20161
  year = 2011
  doi_id = "10.1371/journal.pone.0020161"
  pmid = 21731610
}

citation {
  article_id = sceds
  authors = McCoy AJ, Nicholls RA, Schneider TR
  title = SCEDS: protein fragments for molecular replacement in Phaser
  year = 2013
  journal = Acta Cryst. D
  volume = 69
  doi_id = "10.1107/S0907444913021811"
}

citation {
  article_id = mrage
  authors = Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ
  title = Phaser.MRage: automated molecular replacement.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 69
  pages = 2276-86
  year = 2013
  doi_id = "10.1107/S0907444913022750"
  pmid = 24189240
}

citation {
  article_id = anneal_omit
  authors = Hodel A, Kim SH, Brunger AT
  title = Model bias in macromolecular crystal structures
  year = 1992
  journal = Acta Cryst. A
  volume = 48
  pages = 851-858
  doi_id = doi:10.1107/S0108767392006044
}

citation {
  article_id = bss2
  authors = Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A
  title = Bulk-solvent and overall scaling revisited: faster calculations, improved results.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 69
  pages = 625-34
  year = 2013
  doi_id = "10.1107/S0907444913000462"
  pmid = 23519671
}

citation {
  article_id = brunger_rfree
  authors = Brünger AT
  title = Free R value: a novel statistical quantity for assessing the accuracy of crystal structures.
  journal = Nature
  volume = 355
  pages = 472-5
  year = 2008
  doi_id = doi:10.1038/355472a0
  pmid = 18481394
  external = True
}

citation {
  article_id = brunger_anneal
  authors = Brünger AT, Kuriyan J, Karplus M
  title = Crystallographic R factor refinement by molecular dynamics.
  journal = Science
  volume = 235
  pages = 458-60
  year = 1987
  doi_id = "10.1126/science.235.4787.458"
  pmid = 17810339
}

citation {
  article_id = mccoy_likelihood
  authors = McCoy AJ
  title = Liking likelihood.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 60
  pages = 2169-83
  year = 2004
  doi_id = "10.1107/S0907444904016038"
  pmid = 15572770
}

citation {
  article_id = zwart_pseudosymm
  authors = Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD
  title = Surprises and pitfalls arising from (pseudo)symmetry.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 64
  pages = 99-107
  year = 2008
  doi_id = "10.1107/S090744490705531X"
  pmid = 18094473
}

citation {
  article_id = ramachandran
  authors = Ramachandran GN, Ramakrishnan C, Sasisekharan V
  title = Stereochemistry of polypeptide chain configurations.
  journal = J Mol Biol
  volume = 7
  pages = 95-9
  year = 1963
  doi_id = 10.1016/S0022-2836(63)80023-6
  pmid = 13990617
}

citation {
  article_id = terwilliger_find_helices
  authors = Terwilliger TC
  title = Rapid model building of alpha-helices in electron-density maps.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 66
  pages = 268-75
  year = 2010
  doi_id = "10.1107/S0907444910000314"
  pmid = 20179338
}

citation {
  article_id = terwilliger_find_sheets
  authors = Terwilliger TC
  title = Rapid model building of beta-sheets in electron-density maps.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 66
  pages = 276-84
  year = 2010
  doi_id = "10.1107/S0907444910000302"
  pmid = 20179339
}

citation {
  article_id = terwilliger_trace_chain
  authors = Terwilliger TC
  title = Rapid chain tracing of polypeptide backbones in electron-density maps.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 66
  pages = 285-94
  year = 2010
  doi_id = "10.1107/S0907444910000272"
  pmid = 20179340
}

citation {
  article_id = read_sigmaa
  authors = Read RJ
  title = Improved Fourier coefficients for maps using phases from partial structures with errors.
  journal = Acta Crystallographica
  volume = 42
  year = 1986
  pages = 140-149
  doi_id =  doi:10.1107/S0108767386099622
}

citation {
  article_id = mpscore
  authors = Keedy DA, Williams CJ, Headd JJ, Arendall WB, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS
  title = The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.
  journal = Proteins
  volume = 77 Suppl 9
  pages = 29-49
  year = 2009
  doi_id = "10.1002/prot.22551"
  pmid = 19731372
}

citation {
  article_id = lovell_geometry
  authors = Lovell SC, Davis IW, Arendall WB, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC
  title = Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
  journal = Proteins
  volume = 50
  year = 2003
  pages = 437-50
  doi_id = "10.1002/prot.10286"
  pmid = 12557186
}

citation {
  article_id = ncs_from_density
  authors = Terwilliger TC
  title = Finding non-crystallographic symmetry in density maps of macromolecular structures.
  journal = J Struct Funct Genomics
  volume = 14
  pages = 91-5
  year = 2013
  doi_id = "10.1007/s10969-013-9157-7"
  pmid = 23881095
}

citation {
  article_id = dm_ncs
  authors = Terwilliger TC
  title = Statistical density modification with non-crystallographic symmetry.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 58
  pages = 2082-6
  year = 2002
  doi_id = doi:10.1107/S0907444902016360
  pmid = 12454468
}

citation {
  article_id = resolve
  authors = Terwilliger TC
  title = Maximum-likelihood density modification.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 56
  pages = 965-72
  year = 2000
  doi_id = doi:10.1107/S0907444900005072
  pmid = 10944333
}

citation {
  article_id = map_ml_phase
  authors = Terwilliger TC
  title = Map-likelihood phasing.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 57
  pages = 1763-75
  year = 2001
  doi_id =  doi:10.1107/S0907444901013749
  pmid = 11717488
}

citation {
  article_id = phaser_frf
  authors = Storoni LC, McCoy AJ, Read RJ
  title = Likelihood-enhanced fast rotation functions.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 60
  pages = 432-8
  year = 2004
  doi_id = "10.1107/S0907444903028956"
  pmid = 14993666
}

citation {
  article_id = phaser_ftf
  authors = McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ
  title = Likelihood-enhanced fast translation functions.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 61
  pages = 458-64
  year = 2005
  doi_id = "10.1107/S0907444905001617"
  pmid = 15805601
}


citation {
  article_id = dm_motifs
  authors = Terwilliger TC
  title = Maximum-likelihood density modification using pattern recognition of structural motifs.
  year = 2001
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 57
  pages = 1755-62
  pmid = 11717487
  doi_id = doi:10.1107/S0907444901013737
}

citation {
  article_id = r_meas
  authors = Diederichs K, Karplus PA
  title = Improved R-factors for diffraction data analysis in macromolecular crystallography.
  journal = Nat Struct Biol
  volume = 4
  pages = 269-75
  year = 1997
  doi_id = 10.1038/nsb0497-269
  pmid = 9095194
}

citation {
  article_id = evans_data_reduction
  authors = Evans PR
  title = An introduction to data reduction: space-group determination, scaling and intensity statistics.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 67
  pages = 282-92
  year = 2011
  doi_id = "10.1107/S090744491003982X"
  pmid = 21460446
}

citation {
  article_id = weiss_r_pim
  authors = Weiss MS
  title = Global indicators of data quality
  journal = J. Appl. Cryst.
  volume = 34
  year = 2001
  pages = 130-135
  doi_id = "10.1107/S0021889800018227"
}

citation {
  article_id = cdl
  authors = Berkholz DS, Shapovalov MV, Dunbrack RL, Karplus PA
  title = Conformation dependence of backbone geometry in proteins.
  journal = Structure
  volume = 17
  pages = 1316-25
  year = 2009
  doi_id = "10.1016/j.str.2009.08.012"
  pmid = 19836332
}

citation {
  article_id = cdl_tnt
  authors = Tronrud DE, Berkholz DS, Karplus PA
  title = Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 66
  pages = 834-42
  year = 2010
  doi_id = "10.1107/S0907444910019207"
  pmid = 20606264
}

citation {
  article_id = ssm
  authors = Krissinel E, Henrick K
  title = Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 60
  pages = 2256-68
  year = 2004
  doi_id = "10.1107/S0907444904026460"
  pmid = 15572779
}

citation {
  article_id = leontis_westhof
  authors = Leontis NB, Westhof E
  title = Geometric nomenclature and classification of RNA base pairs.
  journal = RNA
  volume = 7
  pages = 499-512
  year = 2001
  pmid = 11345429
}

citation {
  article_id = sculptor
  authors = Bunkóczi G, Read RJ
  title = Improvement of molecular-replacement models with Sculptor.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 67
  pages = 303-12
  year = 2011
  doi_id = "10.1107/S0907444910051218"
  pmid = 21460448
}

citation {
  article_id = ion_placement
  authors = Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD
  title = Automated identification of elemental ions in macromolecular crystal structures.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 70
  pages = 1104-14
  year = 2014
  doi_id = "10.1107/S1399004714001308"
  pmid = 24699654
}

citation {
  article_id = torsion_ncs
  authors = Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD
  title = Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement.
  journal = Acta Crystallogr D Biol Crystallogr
  volume = 70
  pages = 1346-56
  year = 2014
  doi_id = "10.1107/S1399004714003277"
  pmid = 24816103
}

citation {
  article_id = domain_parser
  authors = Xu Y, Xu D, Gabow HN
  title = Protein domain decomposition using a graph-theoretic approach.
  journal = Bioinformatics
  volume = 16
  pages = 1091-1104
  year = 2000
  doi_id = "10.1093/bioinformatics/16.12.1091"
  pmid = 11159328
}

citation {
  article_id = stoer_wagner_min_cut
  authors = Stoer M, Wagner F
  title = A simple min-cut algorithm.
  journal = Journal of the ACM
  volume = 44
  pages = 585-591
  year = 1997
  doi_id = "10.1145/263867.263872"
}

citation {
  article_id = boykov_kolmogorov_max_flow
  authors = Boykov Y, Kolmogorov V
  title = An Experimental Comparison of Min-Cut/Max-Flow Algorithms for Energy Minimization in Vision.
  journal = IEEE Transactions on Pattern Analysis and Machine Intelligence
  volume = 26
  pages = 1124-1137
  year = 2004
}

citation {
  article_id = graph_cut_enumeration
  authors = Yeh L-P, Wang B-F, Su H-H
  title = Efficient Algorithms for the Problems of Enumerating Cut by Non-decreasing Weights
  journal = Algoritmica
  volume = 5626
  pages = 297-312
  year = 2010
}

citation {
  article_id = fem
  authors = Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD
  title = FEM: feature-enhanced map
  journal = Acta Cryst. D
  volume = 71
  pages = 646-666
  year = 2015
}

citation {
  article_id = tech_parallelity
  authors = Sobolev OV, Afonine PV, Adams PD, Urzhumtsev A
  title = Programming new geometry restraints: parallelity of atomic groups
  journal = J. Appl. Cryst.
  volume = 48
  pages = 1130-1141
  year = 2015
}

citation {
  article_id = phenix.real_space_refine_CCN
  authors = Afonine PV,  Headd JJ, Terwilliger TC, Adams PD
  title = New tool: phenix.real_space_refine
  journal = Computational Crystallography Newsletter
  volume = 4
  pages = 43-44
  year = 2013
}

citation {
  article_id = phenix.real_space_refine
  authors = Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD
  title = Real-space refinement in PHENIX for cryo-EM and crystallography
  journal = Acta Cryst. D
  volume = 74
  pages = 531-544
  year = 2018
  doi_id = 10.1107/S2059798318006551
}

citation {
  article_id = phenix.validation_cryoem
  authors = Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A
  title = New tools for the analysis and validation of cryo-EM maps and atomic models
  journal = Acta Cryst. D
  volume = 74
  pages = 814-840
  year = 2018
  doi_id = 10.1107/S2059798318009324
}

citation {
  article_id = phenix.polder
  authors = Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD
  title = Polder maps: improving OMIT maps by excluding bulk solvent
  journal = Acta Cryst. D
  volume = 73
  pages = 148-157
  year = 2017
  doi_id = "10.1107/S2059798316018210"
  pmid = 28177311
}

citation {
  article_id = resolve_cryo_em
  authors = Terwilliger TC, Ludtke SJ, Read RJ, Adams PD, Afonine
  title = Improvement of cryo-EM maps by density modification
  year = 2020
  journal = Nature Methods
  volume = 17
  pages = 923-927
  pmid = 32807957
  doi_id = 10.1038/s41592-020-0914-9
}

citation {
  article_id = autosharpen
  authors = Terwilliger TC, Afonine PV, Sobolev, OV, Adams PD
  title = Automated map sharpening by maximization of detail and connectivity
  year = 2018
  journal = Acta Cryst. D
  volume = 74
  pages = 545-559
  pmid = 29872005
  doi_id = 10.1107/S2059798318004655
}

citation {
  article_id = map_to_model
  authors = Terwilliger TC, Adams PD, Afonine PV, Sobolev OV
  title = A fully automatic method yielding initial models from high-resolution electron cryo-microscopy maps
  year = 2019
  journal = Nature Methods
  volume = 15
  pages = 905-9080
  pmid = 30377346
  doi_id = 10.1038/s41592-018-0173-1
}

citation {
  article_id = map_to_model_2
  authors = Terwilliger TC, Adams PD, Afonine PV, Sobolev OV
  title = Cryo-EM map interpretation and protein model-building using iterative map segmentation
  year = 2020
  journal = Protein Science
  volume = 29
  pages = 87-99
  pmid = 31599033
  doi_id = 10.1002/pro.3740
}


citation {
  article_id = sequence_from_map
  authors = Terwilliger TC, Sobolev OV, Afonine, PV, Adams PD, Ho, CM, Li, X, Zhou, ZH
  title = Protein identification from electron cryomicroscopy maps by automated model-building and side-chain matching
  year = 2021
  journal = Acta Cryst D.
  volume = 77
  pages = 457-462
  pmid = 33825706
  doi_id = 10.1107/S2059798321001765
}

citation {
  article_id = cryo_model_challenge
  authors = Richardson JS, Williams CJ, Videau LL, Chen VB, Richardson DC
  title = Assessment of detailed conformations suggests strategies for improving cryoEM models: helix at lower resolution, ensembles, pre-refinement fixups, and validation at a multi-residue length scale
  year = 2018
  journal = Struct Biol
  volume = 204
  pages = 319-328
  pmid = 30107233
  doi_id = 10.1016/j.jsb.2018.08.007
}

citation {
  article_id = helix_cap
  authors = Richardson JS, Richardson DC
  title = Amino acid preferences for specific locations at the ends of alpha helices
  year = 1988
  journal = Science
  volume = 240(4859)
  pages = 1648-52
  pmid = 3381086
  doi_id = 10.1126/science.3381086
}

citation {
  article_id = beta_bulge
  authors = Richardson JS, Getzoff ED, Richardson DC
  title = The beta bulge: a common small unit of nonrepetitive protein structure
  year = 1978
  journal = PNAS
  volume = 75(6)
  pages = 2574-8
  pmid = 275827
  doi_id = 10.1073/pnas.75.6.2574
}

citation {
  article_id = isolde
  authors = Croll TI
  title = ISOLDE: a physically realistic environment for model building into low‐resolution electron‐density maps
  year = 2018
  journal = Acta Cryst. D
  volume = 74(6)
  pages = 519-30
  pmid = None
  doi_id = 10.1107/S2059798318002425
}

citation {
  article_id = mmcif_deposition
  authors = 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, Westboork J, Wojdyr M, Yokochi M, Young JY
  title = Announcing mandatory submission of PDBx/mmCIF format files for \
    crystallographic depositions to the Protein Data Bank (PDB)
  year = 2019
  journal = Acta Cryst. D
  volume = 75
  pages = 451-454
  pmid = 30988261
  doi_id = 10.1107/S2059798319004522
}

citation {
  article_id = find_alt_orig_sym_mate
  authors = Oeffner RD, Bunkóczi G, Read RJ
  title = phenix.find_alt_orig_sym_mate
  journal = Computational Crystallography Newsletter
  volume = 3
  pages = 5-10
  year = 2012
}

citation {
  article_id = hklviewer
  authors = Oeffner RD, McCoy AJ, Stockwell DH, Sammito MD, Hatti KS,Croll TI, Read RJ
  title = HKLviewer, a new 3D reflection data viewer for CCTBX
  journal = Computational Crystallography Newsletter
  volume = 12
  pages = 15-25
  year = 2021
}
