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Afonine, Pavel

TitleComputer Research Sci/Engr
InstitutionLawrence Berkeley National Lab
DepartmentMolecular Biophys & Integ Bio
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/221-7384
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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. Afonine P, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol. 2018 Jun 01; 74(Pt 6):531-544. PMID: 29872004.
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    2. Terwilliger TC, Sobolev OV, Afonine P, Adams PD. Automated map sharpening by maximization of detail and connectivity. Acta Crystallogr D Struct Biol. 2018 Jun 01; 74(Pt 6):545-559. PMID: 29872005.
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    3. Oeffner RD, Afonine P, Millán C, Sammito M, Usón I, Read RJ, McCoy AJ. On the application of the expected log-likelihood gain to decision making in molecular replacement. Acta Crystallogr D Struct Biol. 2018 Apr 01; 74(Pt 4):245-255. PMID: 29652252.
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    4. Altan I, Fusco D, Afonine P, Charbonneau P. Learning about Biomolecular Solvation from Water in Protein Crystals. J Phys Chem B. 2018 03 08; 122(9):2475-2486. PMID: 29397724.
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    5. Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine P, 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.
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    6. Zheng M, Moriarty NW, Xu Y, Reimers JR, Afonine P, 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.
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    7. Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine P, 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.
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    8. Greber BJ, Nguyen THD, Fang J, Afonine P, Adams PD, Nogales E. The cryo-electron microscopy structure of human transcription factor IIH. Nature. 2017 09 21; 549(7672):414-417. PMID: 28902838.
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    9. Hryc CF, Chen DH, Afonine P, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams PD, King JA, Schmid MF, Chiu W. Accurate model annotation of a near-atomic resolution cryo-EM map. Proc Natl Acad Sci U S A. 2017 03 21; 114(12):3103-3108. PMID: 28270620.
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    10. Liebschner D, Afonine P, Moriarty NW, 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.
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    11. Lokareddy RK, Sankhala RS, Roy A, Afonine P, Motwani T, Teschke CM, Parent KN, Cingolani G. Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation. Nat Commun. 2017 Jan 30; 8:14310. PMID: 28134243.
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    12. Zheng M, Reimers JR, Waller MP, Afonine P. Q|R: quantum-based refinement. Acta Crystallogr D Struct Biol. 2017 Jan 01; 73(Pt 1):45-52. PMID: 28045384.
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    13. 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 NW, Liebschner D, Afonine P, 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.
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    14. Urzhumtsev A, Afonine P, Van Benschoten AH, Fraser JS, Adams PD. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum. Acta Crystallogr D Struct Biol. 2016 Sep 01; 72(Pt 9):1073-1075. PMID: 27599739.
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    15. Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine P, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL, Bardwell JC. Visualizing chaperone-assisted protein folding. Nat Struct Mol Biol. 2016 07; 23(7):691-7. PMID: 27239796; PMCID: PMC4937829 [Available on 11/30/16].
    16. McCullough J, Clippinger AK, Talledge N, Skowyra ML, Saunders MG, Naismith TV, Colf LA, Afonine P, Arthur C, Sundquist WI, Hanson PI, Frost A. Structure and membrane remodeling activity of ESCRT-III helical polymers. Science. 2015 Dec 18; 350(6267):1548-51. PMID: 26634441; PMCID: PMC4684769.
    17. Urzhumtsev A, Afonine P, 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; 71(Pt 8):1668-83. PMID: 26249348; PMCID: PMC4528800.
    18. Van Benschoten AH, Afonine P, 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; 71(Pt 8):1657-67. PMID: 26249347; PMCID: PMC4528799.
    19. Sobolev OV, Afonine P, Adams PD, Urzhumtsev A. Programming new geometry restraints: parallelity of atomic groups. J Appl Crystallogr. 2015 Aug 01; 48(Pt 4):1130-1141. PMID: 26306091.
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    20. Weichenberger CX, Afonine P, Kantardjieff K, Rupp B. The solvent component of macromolecular crystals. Acta Crystallogr D Biol Crystallogr. 2015 May; 71(Pt 5):1023-38. PMID: 25945568; PMCID: PMC4427195.
    21. Afonine P, 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; 71(Pt 3):646-66. PMID: 25760612; PMCID: PMC4356370.
    22. Urzhumtsev A, Afonine P, Lunin VY, Terwilliger TC, Adams PD. Metrics for comparison of crystallographic maps. Acta Crystallogr D Biol Crystallogr. 2014 Oct; 70(Pt 10):2593-606. PMID: 25286844; PMCID: PMC4188004.
    23. Wang Z, Hryc CF, Bammes B, Afonine P, 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 Sep 04; 5:4808. PMID: 25185801; PMCID: PMC4155512.
    24. Headd JJ, Echols N, Afonine P, 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. PMID: 24816103; PMCID: PMC4014122.
    25. Echols N, Morshed N, Afonine P, 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; 70(Pt 4):1104-14. PMID: 24699654.
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    26. Echols N, Moriarty NW, Klei HE, Afonine P, 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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    27. Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine P, Hung LW. Model morphing and sequence assignment after molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013 Nov; 69(Pt 11):2244-50. PMID: 24189236.
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    28. Nwachukwu JC, Southern MR, Kiefer JR, Afonine P, Adams PD, Terwilliger TC, Nettles KW. Improved crystallographic structures using extensive combinatorial refinement. Structure. 2013 Nov 05; 21(11):1923-30. PMID: 24076406; PMCID: PMC4070946.
    29. Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine P, 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. PMID: 23840063; PMCID: PMC3725109.
    30. Urzhumtsev A, Afonine P, Adams PD. TLS from fundamentals to practice. Crystallogr Rev. 2013 Jul 01; 19(4):230-270. PMID: 25249713.
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    31. Afonine P, 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. PMID: 23519671; PMCID: PMC3606040.
    32. Burnley BT, Afonine P, Adams PD, Gros P. Modelling dynamics in protein crystal structures by ensemble refinement. Elife. 2012 Dec 18; 1:e00311. PMID: 23251785; PMCID: PMC3524795.
    33. Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine P, 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. PMID: 22751672.
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    34. Echols N, Grosse-Kunstleve RW, Afonine P, 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 Crystallogr. 2012 Jun 01; 45(Pt 3):581-586. PMID: 22675231.
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    35. Afonine P, 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. PMID: 22505256; PMCID: PMC3322595.
    36. Headd JJ, Echols N, Afonine P, 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. PMID: 22505258; PMCID: PMC3322597.
    37. Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine P, Echols N. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J Struct Funct Genomics. 2012 Jun; 13(2):81-90. PMID: 22418934.
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    38. Adams PD, Afonine P, 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. PMID: 21821126.
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    39. Czerwinski A, Valenzuela F, Afonine P, Dauter M, Dauter Z. N-{N-[2-(3,5-Difluorophenyl)acetyl]-(S)-alanyl}-(S)-phenylglycine tert-butyl ester (DAPT): an inhibitor of ?-secretase, revealing fine electronic and hydrogen-bonding features. Acta Crystallogr C. 2010 Dec; 66(Pt 12):o585-8. PMID: 21123889; PMCID: PMC3014104.
    40. Afonine P, 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. PMID: 21041930; PMCID: PMC2967420.
    41. Bruning JB, Parent AA, Gil G, Zhao M, Nowak J, Pace MC, Smith CL, Afonine P, 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. PMID: 20924370; PMCID: PMC2974172.
    42. Kohn JE, Afonine P, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol. 2010 Aug 26; 6(8). PMID: 20865158; PMCID: PMC2928775.
    43. Afonine P, 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 Crystallogr. 2010 Aug 01; 43(Pt 4):669-676. PMID: 20648263.
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    44. Adams PD, Afonine P, 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. PMID: 20124702.
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    45. Tomanicek SJ, Blakeley MP, Cooper J, Chen Y, Afonine P, Coates L. Neutron diffraction studies of a class A beta-lactamase Toho-1 E166A/R274N/R276N triple mutant. J Mol Biol. 2010 Mar 05; 396(4):1070-80. PMID: 20036259.
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    46. Urzhumtsev A, Afonine P, 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. PMID: 19966414; PMCID: PMC2789003.
    47. Adams PD, Afonine P, 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. PMID: 19700309.
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    48. Pražnikar J, Afonine P, 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. PMID: 19690370; PMCID: PMC2733881.
    49. Afonine P, Grosse-Kunstleve RW, Urzhumtsev A, Adams PD. Automatic multiple-zone rigid-body refinement with a large convergence radius. J Appl Crystallogr. 2009 Aug 01; 42(Pt 4):607-615. PMID: 19649324.
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    50. Terwilliger TC, Adams PD, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine P, 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.
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    51. Adams PD, Mustyakimov M, Afonine P, 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. PMID: 19465771; PMCID: PMC2685734.
    52. Urzhumtseva L, Afonine P, Adams PD, Urzhumtsev A. Crystallographic model quality at a glance. Acta Crystallogr D Biol Crystallogr. 2009 Mar; 65(Pt 3):297-300. PMID: 19237753; PMCID: PMC2651759.
    53. Terwilliger TC, Grosse-Kunstleve RW, Afonine P, 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. PMID: 18453687; PMCID: PMC2424225.
    54. Langan P, Fisher Z, Kovalevsky A, Mustyakimov M, Sutcliffe Valone A, Unkefer C, Waltman MJ, Coates L, Adams PD, Afonine P, Bennett B, Dealwis C, Schoenborn BP. Protein structures by spallation neutron crystallography. J Synchrotron Radiat. 2008 May; 15(Pt 3):215-8. PMID: 18421142; PMCID: PMC2394804.
    55. Blakeley MP, Ruiz F, Cachau R, Hazemann I, Meilleur F, Mitschler A, Ginell S, Afonine P, Ventura ON, Cousido-Siah A, Haertlein M, Joachimiak A, Myles D, Podjarny A. Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase. Proc Natl Acad Sci U S A. 2008 Feb 12; 105(6):1844-8. PMID: 18250329; PMCID: PMC2538850.
    56. Zwart PH, Afonine P, 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. PMID: 18542881.
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    57. Terwilliger TC, Grosse-Kunstleve RW, Afonine P, 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. PMID: 18094468; PMCID: PMC2394820.
    58. Afonine P, 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. PMID: 18007035; PMCID: PMC2808317.
    59. Terwilliger TC, Grosse-Kunstleve RW, Afonine P, 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. PMID: 17452785; PMCID: PMC2483474.
    60. Afonine P, 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. PMID: 15983406; PMCID: PMC2808320.
    61. Afonine P, Lunin VY, Muzet N, Urzhumtsev A. On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps. Acta Crystallogr D Biol Crystallogr. 2004 Feb; 60(Pt 2):260-74. PMID: 14747702.
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    62. Afonine P, Urzhumtsev A. On a fast calculation of structure factors at a subatomic resolution. Acta Crystallogr A. 2004 Jan; 60(Pt 1):19-32. PMID: 14691324.
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    63. Lunin VY, Afonine P, Urzhumtsev AG. Likelihood-based refinement. I. Irremovable model errors. Acta Crystallogr A. 2002 May; 58(Pt 3):270-82. PMID: 11961289.
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