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Items: 1 to 50 of 72

1.

Including crystallographic symmetry in quantum-based refinement: Q|R#2.

Zheng M, Biczysko M, Xu Y, Moriarty NW, Kruse H, Urzhumtsev A, Waller MP, Afonine PV.

Acta Crystallogr D Struct Biol. 2020 Jan 1;76(Pt 1):41-50. doi: 10.1107/S2059798319015122. Epub 2020 Jan 1.

PMID:
31909742
2.

Cryo-EM map interpretation and protein model-building using iterative map segmentation.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

Protein Sci. 2020 Jan;29(1):87-99. doi: 10.1002/pro.3740. Epub 2019 Oct 24.

3.

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.

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.

Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877. doi: 10.1107/S2059798319011471. Epub 2019 Oct 2.

4.

Cryo_fit: Democratization of flexible fitting for cryo-EM.

Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K.

J Struct Biol. 2019 Oct 1;208(1):1-6. doi: 10.1016/j.jsb.2019.05.012. Epub 2019 Jul 3.

PMID:
31279069
5.

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB).

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.

Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):451-454. doi: 10.1107/S2059798319004522. Epub 2019 Apr 8. No abstract available.

PMID:
30988261
6.

Anomalous X-ray diffraction studies of ion transport in K+ channels.

Langan PS, Vandavasi VG, Weiss KL, Afonine PV, El Omari K, Duman R, Wagner A, Coates L.

Nat Commun. 2018 Oct 31;9(1):4540. doi: 10.1038/s41467-018-06957-w.

7.

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

Nat Methods. 2018 Nov;15(11):905-908. doi: 10.1038/s41592-018-0173-1. Epub 2018 Oct 30.

8.

Reply to 'Misreading chaperone-substrate complexes from random noise'.

Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL 3rd, Bardwell JCA.

Nat Struct Mol Biol. 2018 Nov;25(11):990-991. doi: 10.1038/s41594-018-0145-2. No abstract available.

PMID:
30297780
9.

New tools for the analysis and validation of cryo-EM maps and atomic models.

Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A.

Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):814-840. doi: 10.1107/S2059798318009324. Epub 2018 Sep 3.

10.

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition.

Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):800-813. doi: 10.1107/S2059798318004588. Epub 2018 Jul 24. Review.

11.

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge.

Terwilliger TC, Adams PD, Afonine PV, Sobolev OV.

J Struct Biol. 2018 Nov;204(2):338-343. doi: 10.1016/j.jsb.2018.07.016. Epub 2018 Jul 29.

12.

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation.

Afonine PV, Adams PD, Urzhumtsev A.

Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):621-631. doi: 10.1107/S2059798318005764. Epub 2018 Jun 8.

13.

Automated map sharpening by maximization of detail and connectivity.

Terwilliger TC, Sobolev OV, Afonine PV, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):545-559. doi: 10.1107/S2059798318004655. Epub 2018 May 18.

14.

Real-space refinement in PHENIX for cryo-EM and crystallography.

Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD.

Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi: 10.1107/S2059798318006551. Epub 2018 May 30.

15.

On the application of the expected log-likelihood gain to decision making in molecular replacement.

Oeffner RD, Afonine PV, Millán C, Sammito M, Usón I, Read RJ, McCoy AJ.

Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):245-255. doi: 10.1107/S2059798318004357. Epub 2018 Apr 4.

16.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM.

J Appl Crystallogr. 2018 Feb 1;51(Pt 1):193-199. doi: 10.1107/S1600576717015825. eCollection 2018 Feb 1.

17.

Learning about Biomolecular Solvation from Water in Protein Crystals.

Altan I, Fusco D, Afonine PV, Charbonneau P.

J Phys Chem B. 2018 Mar 8;122(9):2475-2486. doi: 10.1021/acs.jpcb.7b09898. Epub 2018 Feb 21.

PMID:
29397724
18.

Solving the scalability issue in quantum-based refinement: Q|R#1.

Zheng M, Moriarty NW, Xu Y, Reimers JR, Afonine PV, Waller MP.

Acta Crystallogr D Struct Biol. 2017 Dec 1;73(Pt 12):1020-1028. doi: 10.1107/S2059798317016746. Epub 2017 Nov 30.

19.

The cryo-electron microscopy structure of human transcription factor IIH.

Greber BJ, Nguyen THD, Fang J, Afonine PV, Adams PD, Nogales E.

Nature. 2017 Sep 21;549(7672):414-417. doi: 10.1038/nature23903. Epub 2017 Sep 13.

20.

Interactive comparison and remediation of collections of macromolecular structures.

Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd JJ, Poon BK, Adams PD.

Protein Sci. 2018 Jan;27(1):182-194. doi: 10.1002/pro.3296. Epub 2017 Nov 11.

21.

Accurate model annotation of a near-atomic resolution cryo-EM map.

Hryc CF, Chen DH, Afonine PV, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams PD, King JA, Schmid MF, Chiu W.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3103-3108. doi: 10.1073/pnas.1621152114. Epub 2017 Mar 7.

22.

Polder maps: improving OMIT maps by excluding bulk solvent.

Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD.

Acta Crystallogr D Struct Biol. 2017 Feb 1;73(Pt 2):148-157. doi: 10.1107/S2059798316018210. Epub 2017 Feb 1.

23.

Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation.

Lokareddy RK, Sankhala RS, Roy A, Afonine PV, Motwani T, Teschke CM, Parent KN, Cingolani G.

Nat Commun. 2017 Jan 30;8:14310. doi: 10.1038/ncomms14310.

24.

Q|R: quantum-based refinement.

Zheng M, Reimers JR, Waller MP, Afonine PV.

Acta Crystallogr D Struct Biol. 2017 Jan 1;73(Pt 1):45-52. doi: 10.1107/S2059798316019847. Epub 2017 Jan 1.

25.

Structure of photosystem II and substrate binding at room temperature.

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 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.

Nature. 2016 Dec 15;540(7633):453-457. doi: 10.1038/nature20161. Epub 2016 Nov 21.

26.

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.

Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD.

Acta Crystallogr D Struct Biol. 2016 Sep 1;72(Pt 9):1073-1075. Epub 2016 Aug 31.

27.

Visualizing chaperone-assisted protein folding.

Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL 3rd, Bardwell JC.

Nat Struct Mol Biol. 2016 Jul;23(7):691-7. doi: 10.1038/nsmb.3237. Epub 2016 May 30.

28.

Programming new geometry restraints: parallelity of atomic groups.

Sobolev OV, Afonine PV, Adams PD, Urzhumtsev A.

J Appl Crystallogr. 2015 Jul 8;48(Pt 4):1130-1141. eCollection 2015 Aug 1.

29.

From deep TLS validation to ensembles of atomic models built from elemental motions.

Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1668-83. doi: 10.1107/S1399004715011426. Epub 2015 Jul 28. Erratum in: Acta Crystallogr D Struct Biol. 2016 Sep;72(Pt 9):1073-5.

30.

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.

Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS.

Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1657-67. doi: 10.1107/S1399004715007415. Epub 2015 Jul 28.

31.

The solvent component of macromolecular crystals.

Weichenberger CX, Afonine PV, Kantardjieff K, Rupp B.

Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1023-38. doi: 10.1107/S1399004715006045. Epub 2015 Apr 30. Review.

32.

FEM: feature-enhanced map.

Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2015 Mar;71(Pt 3):646-66. doi: 10.1107/S1399004714028132. Epub 2015 Feb 26.

33.

Metrics for comparison of crystallographic maps.

Urzhumtsev A, Afonine PV, Lunin VY, Terwilliger TC, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Oct;70(Pt 10):2593-606. doi: 10.1107/S1399004714016289. Epub 2014 Sep 27.

34.

An atomic model of brome mosaic virus using direct electron detection and real-space optimization.

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.

Nat Commun. 2014 Sep 4;5:4808. doi: 10.1038/ncomms5808.

35.

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement.

Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1346-56. doi: 10.1107/S1399004714003277. Epub 2014 Apr 30.

36.

Automated identification of elemental ions in macromolecular crystal structures.

Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Apr;70(Pt 4):1104-14. doi: 10.1107/S1399004714001308. Epub 2014 Mar 20.

37.

Automating crystallographic structure solution and refinement of protein-ligand complexes.

Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):144-54. doi: 10.1107/S139900471302748X. Epub 2013 Dec 25.

38.

Model morphing and sequence assignment after molecular replacement.

Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Hung LW.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2244-50. doi: 10.1107/S0907444913017770. Epub 2013 Oct 18.

39.

Improved crystallographic structures using extensive combinatorial refinement.

Nwachukwu JC, Southern MR, Kiefer JR, Afonine PV, Adams PD, Terwilliger TC, Nettles KW.

Structure. 2013 Nov 5;21(11):1923-30. doi: 10.1016/j.str.2013.07.025. Epub 2013 Sep 26.

40.

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling.

Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12301-6. doi: 10.1073/pnas.1309947110. Epub 2013 Jul 9.

41.

TLS from fundamentals to practice.

Urzhumtsev A, Afonine PV, Adams PD.

Crystallogr Rev. 2013 Jul 1;19(4):230-270.

42.

Bulk-solvent and overall scaling revisited: faster calculations, improved results.

Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A.

Acta Crystallogr D Biol Crystallogr. 2013 Apr;69(Pt 4):625-34. doi: 10.1107/S0907444913000462. Epub 2013 Mar 14.

43.

Modelling dynamics in protein crystal structures by ensemble refinement.

Burnley BT, Afonine PV, Adams PD, Gros P.

Elife. 2012 Dec 18;1:e00311. doi: 10.7554/eLife.00311.

44.

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement.

Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Grosse-Kunstleve RW, Hung LW.

Acta Crystallogr D Biol Crystallogr. 2012 Jul;68(Pt 7):861-70. doi: 10.1107/S0907444912015636. Epub 2012 Jun 19.

45.

Graphical tools for macromolecular crystallography in PHENIX.

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.

J Appl Crystallogr. 2012 Jun 1;45(Pt 3):581-586. Epub 2012 May 16.

46.

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.

Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):381-90. doi: 10.1107/S0907444911047834. Epub 2012 Mar 16.

47.

Towards automated crystallographic structure refinement with phenix.refine.

Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi: 10.1107/S0907444912001308. Epub 2012 Mar 16.

48.

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.

Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N.

J Struct Funct Genomics. 2012 Jun;13(2):81-90. doi: 10.1007/s10969-012-9129-3. Epub 2012 Mar 15.

49.

The Phenix software for automated determination of macromolecular structures.

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.

Methods. 2011 Sep;55(1):94-106. doi: 10.1016/j.ymeth.2011.07.005. Epub 2011 Jul 29.

50.

Joint X-ray and neutron refinement with phenix.refine.

Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2010 Nov;66(Pt 11):1153-63. doi: 10.1107/S0907444910026582. Epub 2010 Oct 20.

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