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Solving the scalability issue in quantum-based refinement: Q

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

Publikováno v: Zheng, M; Moriarty, NW; Xu, Y; Reimers, JR; Afonine, PV; & Waller, MP. (2017). Solving the scalability issue in quantum-based refinement: Q. Acta Crystallographica Section D: Structural Biology, 73(12), 1020-1028. doi: 10.1107/S2059798317016746. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/7cr4143v

© International Union of Crystallography, 2017. Accurately refining biomacromolecules using a quantum-chemical method is challenging because the cost of a quantum-chemical calculation scales approximately as nm, where n is the number of atoms and m

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http://www.escholarship.org/uc/item/7cr4143v

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The cryo-electron microscopy structure of human transcription factor IIH

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

Publikováno v: Nature, vol 549, iss 7672
Greber, BJ; Nguyen, THD; Fang, J; Afonine, PV; Adams, PD; & Nogales, E. (2017). The cryo-electron microscopy structure of human transcription factor IIH. Nature, 549(7672), 414-417. doi: 10.1038/nature23903. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/4s13w81q

© 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcript

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https://escholarship.org/uc/item/4s13w81q

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Q|R: quantum-based refinement

Autor: Zheng, M, Reimers, JR, Waller, MP, Afonine, PV

Publikováno v: Acta crystallographica. Section D, Structural biology, vol 73, iss Pt 1
Zheng, M; Reimers, JR; Waller, MP; & Afonine, PV. (2017). Q|R: quantum-based refinement. Acta Crystallographica Section D: Structural Biology, 73(1), 45-52. doi: 10.1107/S2059798316019847. UC Irvine: Retrieved from: http://www.escholarship.org/uc/item/3pg313k8

© International Union of Crystallography, 2017. Quantum-based refinement utilizes chemical restraints derived from quantum-chemical methods instead of the standard parameterized library-based restraints used in refinement packages. The motivation is

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https://escholarship.org/uc/item/3pg313k8

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Autor: Zheng, M, Reimers, JR, Waller, MP, Afonine, PV

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______363::5962113c28005b15336c27fda338c72b
https://hdl.handle.net/10453/125272

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From deep TLS validation to ensembles of atomic models built from elemental motions (vol 71, pg 1668, 2015)

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

Publikováno v: Urzhumtsev, A; Afonine, PV; Van Benschoten, AH; Fraser, JS; & Adams, PD. (2016). From deep TLS validation to ensembles of atomic models built from elemental motions (vol 71, pg 1668, 2015). ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 72, 1073-1075. doi: 10.1107/S2059798316013048. UCSF: Retrieved from: http://www.escholarship.org/uc/item/0s2455rk

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http://www.escholarship.org/uc/item/0s2455rk

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

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

Publikováno v: Acta crystallographica. Section D, Biological crystallography, vol 71, iss Pt 8
Van Benschoten, AH; Afonine, PV; Terwilliger, TC; Wall, ME; Jackson, CJ; Sauter, NK; et al.(2015). Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Crystallographica Section D: Biological Crystallography, 71, 1657-1667. doi: 10.1107/S1399004715007415. UCSF: Retrieved from: http://www.escholarship.org/uc/item/8q88m9nn

© 2015 International Union of Crystallography. Identifying the intramolecular motions of proteins and nucleic acids is a major challenge in macromolecular X-ray crystallography. Because Bragg diffraction describes the average positional distribution

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https://escholarship.org/uc/item/8q88m9nn

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FEM: Feature-enhanced map

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

Publikováno v: Afonine, PV; Moriarty, NW; Mustyakimov, M; Sobolev, OV; Terwilliger, TC; Turk, D; et al.(2015). FEM: Feature-enhanced map. Acta Crystallographica Section D: Biological Crystallography, 71, 646-666. doi: 10.1107/S1399004714028132. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/97d776c9

© Afonine et al. 2015. A method is presented that modifies a 2mFobs- D FmodelσA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the sta

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http://www.escholarship.org/uc/item/97d776c9

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