Ab initio solution of macromolecular crystal structures without direct methods

Autor: McCoy, AJ, Oeffner, RD, Wrobel, AG, Ojala, JRM, Tryggvason, K, Lohkamp, B, Read, RJ

The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understan

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f317a230d157c1ee5007379807754153
https://www.repository.cam.ac.uk/handle/1810/264287

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.

Autor: Terwilliger TC; New Mexico Consortium, Los Alamos, NM, USA. tterwilliger@newmexicoconsortium.org.; Los Alamos National Laboratory, Los Alamos, NM, USA. tterwilliger@newmexicoconsortium.org., Liebschner D; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Croll TI; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK., Williams CJ; Department of Biochemistry, Duke University, Durham, NC, USA., McCoy AJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK., Poon BK; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Afonine PV; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Oeffner RD; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK., Richardson JS; Department of Biochemistry, Duke University, Durham, NC, USA., Read RJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK., Adams PD; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Bioengineering, University of California, Berkeley, CA, USA.

Publikováno v: Nature methods [Nat Methods] 2024 Jan; Vol. 21 (1), pp. 110-116. Date of Electronic Publication: 2023 Nov 30.

Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE.

Autor: Oeffner RD; Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom., Croll TI; Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom., Millán C; Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom., Poon BK; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory (LBNL), Building 33R0349, Berkeley, CA 94720-8235, USA., Schlicksup CJ; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory (LBNL), Building 33R0349, Berkeley, CA 94720-8235, USA., Read RJ; Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom., Terwilliger TC; New Mexico Consortium, Los Alamos National Laboratory, 100 Entrada Drive, Los Alamos, NM 87544, USA.

Publikováno v: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2022 Nov 01; Vol. 78 (Pt 11), pp. 1303-1314. Date of Electronic Publication: 2022 Oct 27.

Measuring and using information gained by observing diffraction data.

Autor: Read RJ; Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, England., Oeffner RD; Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, England., McCoy AJ; Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, England.

Publikováno v: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2020 Mar 01; Vol. 76 (Pt 3), pp. 238-247. Date of Electronic Publication: 2020 Feb 25.

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

Autor: Liebschner D; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Afonine PV; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Baker ML; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA., Bunkóczi G; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England., Chen VB; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Croll TI; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England., Hintze B; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Hung LW; Los Alamos National Laboratory, Los Alamos, NM 87545, USA., Jain S; Department of Biochemistry, Duke University, Durham, NC 27710, USA., McCoy AJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England., Moriarty NW; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Oeffner RD; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England., Poon BK; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Prisant MG; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Read RJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England., Richardson JS; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Richardson DC; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Sammito MD; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England., Sobolev OV; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA., Stockwell DH; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, England., Terwilliger TC; Los Alamos National Laboratory, Los Alamos, NM 87545, USA., Urzhumtsev AG; Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 67404 Illkirch, France., Videau LL; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Williams CJ; Department of Biochemistry, Duke University, Durham, NC 27710, USA., Adams PD; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Publikováno v: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2019 Oct 01; Vol. 75 (Pt 10), pp. 861-877. Date of Electronic Publication: 2019 Oct 02.