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Tytuł:
Multivariate estimation of substructure amplitudes for a single-wavelength anomalous diffraction experiment.
Autorzy:
Pannu NS; Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
Skubák P; Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 339-344. Date of Electronic Publication: 2023 Mar 28.
Typ publikacji:
Journal Article
MeSH Terms:
Crystallography, X-Ray*
Czasopismo naukowe
Tytuł:
The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case-study report. Corrigendum.
Autorzy:
Barbarin-Bocahu I; Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France.
Graille M; Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 353. Date of Electronic Publication: 2023 Mar 30.
Typ publikacji:
Published Erratum
Tytuł:
Likelihood-based docking of models into cryo-EM maps.
Autorzy:
Millán C; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
McCoy AJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
Terwilliger TC; New Mexico Consortium, Los Alamos National Laboratory, 100 Entrada Drive, Los Alamos, NM 87544, USA.
Read RJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 281-289. Date of Electronic Publication: 2023 Mar 15.
Typ publikacji:
Journal Article
MeSH Terms:
Proteins*/chemistry
Likelihood Functions ; Models, Molecular ; Cryoelectron Microscopy/methods ; Crystallography, X-Ray ; Protein Conformation
Czasopismo naukowe
Tytuł:
Conformation-dependent ligand hot spots in the spliceosomal RNA helicase BRR2.
Autorzy:
Vester K; Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.
Metz A; Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
Huber S; Drug Design Group, Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
Loll B; Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.
Wahl MC; Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 304-317. Date of Electronic Publication: 2023 Apr 28.
Typ publikacji:
Journal Article
MeSH Terms:
RNA Helicases*/chemistry
RNA Helicases*/genetics
RNA Helicases*/metabolism
Spliceosomes*/genetics
Spliceosomes*/metabolism
Ligands ; DNA Helicases/metabolism ; Protein Conformation ; Binding Sites ; Protein Binding
Czasopismo naukowe
Tytuł:
Buccaneer model building with neural network fragment selection.
Autorzy:
Alharbi E; Department of Computer Science, University of York, Heslington, York YO10 5GH, United Kingdom.
Calinescu R; Department of Computer Science, University of York, Heslington, York YO10 5GH, United Kingdom.
Cowtan K; Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 326-338. Date of Electronic Publication: 2023 Mar 28.
Typ publikacji:
Journal Article
MeSH Terms:
Proteins*/chemistry
Software*
Protein Conformation ; Models, Molecular ; Crystallography, X-Ray ; Neural Networks, Computer
Czasopismo naukowe
Tytuł:
Ambient temperature structure of phosphoketolase from Bifidobacterium longum determined by serial femtosecond X-ray crystallography.
Autorzy:
Nakata K; Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan.
Kashiwagi T; Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan.
Kunishima N; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Naitow H; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Matsuura Y; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Miyano H; Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan.
Mizukoshi T; Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan.
Tono K; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Yabashi M; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Nango E; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Iwata S; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 290-303. Date of Electronic Publication: 2023 Mar 28.
Typ publikacji:
Journal Article
MeSH Terms:
Thiamine Pyrophosphate*/chemistry
Thiamine Pyrophosphate*/metabolism
Bifidobacterium longum*/metabolism
Crystallography, X-Ray ; Transketolase/chemistry ; Transketolase/metabolism ; Phosphoenolpyruvate ; Temperature ; Xylulose ; Catalytic Domain ; Fructose
Czasopismo naukowe
Tytuł:
Introduction to the virtual thematic issue on room-temperature biological crystallography.
Autorzy:
Steiner RA; King's College London, New Hunt's House - Guy's Campus, London SE1 1UL, United Kingdom.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 268-270. Date of Electronic Publication: 2023 Mar 31.
Typ publikacji:
Journal Article
MeSH Terms:
Crystallography*
Temperature ; Crystallography, X-Ray
Czasopismo naukowe
Tytuł:
Structures of L-proline trans-hydroxylase reveal the catalytic specificity and provide deeper insight into AKG-dependent hydroxylation.
Autorzy:
Hu X; Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People's Republic of China.
Huang X; Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People's Republic of China.
Liu J; Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Tianjin, People's Republic of China.
Zheng P; Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Tianjin, People's Republic of China.
Gong W; Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People's Republic of China.
Yang L; Department of Life Sciences and Medicine, University of Science and Technology of China, Hefei, People's Republic of China.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 318-325. Date of Electronic Publication: 2023 Mar 28.
Typ publikacji:
Journal Article
MeSH Terms:
Proline*/chemistry
Prolyl Hydroxylases*/chemistry
Prolyl Hydroxylases*/metabolism
Mixed Function Oxygenases/metabolism ; Ketoglutaric Acids ; Hydroxylation
Czasopismo naukowe
Tytuł:
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps.
Autorzy:
Read RJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
Millán C; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
McCoy AJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
Terwilliger TC; New Mexico Consortium, Los Alamos National Laboratory, 100 Entrada Drive, Los Alamos, NM 87544, USA.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 271-280. Date of Electronic Publication: 2023 Mar 15.
Typ publikacji:
Journal Article
MeSH Terms:
Cryoelectron Microscopy*
Likelihood Functions ; Models, Molecular ; Crystallography
Czasopismo naukowe
Tytuł:
The structure of the complex between the arsenite oxidase from Pseudorhizobium banfieldiae sp. strain NT-26 and its native electron acceptor cytochrome c 552 .
Autorzy:
Poddar N; School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia.
Santini JM; Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.
Maher MJ; School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Apr 01; Vol. 79 (Pt 4), pp. 345-352. Date of Electronic Publication: 2023 Mar 30.
Typ publikacji:
Journal Article
MeSH Terms:
Cytochromes c*/metabolism
Arsenites*/metabolism
Electrons ; Oxidation-Reduction
Czasopismo naukowe
Tytuł:
Accelerating crystal structure determination with iterative AlphaFold prediction.
Autorzy:
Terwilliger TC; New Mexico Consortium, Los Alamos, NM 87544, USA.
Afonine PV; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Liebschner D; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Croll TI; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
McCoy AJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
Oeffner RD; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
Williams CJ; Department of Biochemistry, Duke University, Durham, NC 27710, USA.
Poon BK; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Richardson JS; Department of Biochemistry, Duke University, Durham, NC 27710, USA.
Read RJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom.
Adams PD; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Mar 01; Vol. 79 (Pt 3), pp. 234-244. Date of Electronic Publication: 2023 Feb 27.
Typ publikacji:
Journal Article
MeSH Terms:
Artificial Intelligence*
Crystallography ; Databases, Protein ; Models, Structural
Czasopismo naukowe
Tytuł:
Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures.
Autorzy:
Doukov T; SMB, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Herschlag D; Deparment of Biochemistry, Stanford University, Stanford, CA 94305, USA.
Yabukarski F; Deparment of Biochemistry, Stanford University, Stanford, CA 94305, USA.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Mar 01; Vol. 79 (Pt 3), pp. 212-223. Date of Electronic Publication: 2023 Feb 27.
Typ publikacji:
Journal Article
MeSH Terms:
Data Accuracy*
Endopeptidase K ; Temperature ; Protein Conformation ; Crystallography, X-Ray
Czasopismo naukowe
Tytuł:
20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening.
Autorzy:
Lynch ML; Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
Snell ME; Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
Potter SA; Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
Snell EH; Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
Bowman SEJ; Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Mar 01; Vol. 79 (Pt 3), pp. 198-205. Date of Electronic Publication: 2023 Feb 27.
Typ publikacji:
Journal Article
MeSH Terms:
Biomedical Research*
Robotics*
Crystallization ; High-Throughput Screening Assays ; Models, Structural
Czasopismo naukowe
Tytuł:
Correction of rhodopsin serial crystallography diffraction intensities for a lattice-translocation defect.
Autorzy:
Rodrigues MJ; Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
Casadei CM; Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
Weinert T; Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
Panneels V; Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
Schertler GFX; Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Mar 01; Vol. 79 (Pt 3), pp. 224-233. Date of Electronic Publication: 2023 Feb 27.
Typ publikacji:
Journal Article
Czasopismo naukowe
Tytuł:
A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53.
Autorzy:
Bernardo N; Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain.
Crespo I; Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain.
Cuppari A; Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain.
Meijer WJJ; Centro de Biología Molecular `Severo Ochoa' (CSIC-UAM), Universidad Autónoma de Madrid, Calle Nicolás Cabrera 1, Canto Blanco, 28049 Madrid, Spain.
Boer DR; Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Catalunya, Spain.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Mar 01; Vol. 79 (Pt 3), pp. 259-267. Date of Electronic Publication: 2023 Mar 01.
Typ publikacji:
Journal Article
MeSH Terms:
Eukaryota*
Bacillus*
Humans ; Tumor Suppressor Protein p53 ; Bacillus subtilis ; Transcription Factors ; DNA
Czasopismo naukowe
Tytuł:
Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7.
Autorzy:
Prolič-Kalinšek M; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
Volkov AN; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
Hadži S; Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.
Van Dyck J; Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerpen, Belgium.
Bervoets I; Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
Charlier D; Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
Loris R; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Mar 01; Vol. 79 (Pt 3), pp. 245-258. Date of Electronic Publication: 2023 Feb 27.
Typ publikacji:
Journal Article
MeSH Terms:
Prophages*
Escherichia coli O157*
DNA-Binding Proteins ; Protein Domains ; DNA
Czasopismo naukowe
Tytuł:
Errors in structural biology are not the exception.
Autorzy:
Gao Y; Insitut für Nanostruktur und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Thorn V; 90489 Nürnberg, Germany.
Thorn A; Insitut für Nanostruktur und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Mar 01; Vol. 79 (Pt 3), pp. 206-211. Date of Electronic Publication: 2023 Feb 27.
Typ publikacji:
Journal Article
MeSH Terms:
COVID-19*
Humans ; Pandemics ; SARS-CoV-2 ; Databases, Protein ; Biology
Czasopismo naukowe
Tytuł:
In situ ligand restraints from quantum-mechanical methods.
Autorzy:
Liebschner D; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Moriarty NW; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Poon BK; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Adams PD; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Feb 01; Vol. 79 (Pt 2), pp. 100-110. Date of Electronic Publication: 2023 Jan 20.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Proteins*/chemistry
Protein Conformation ; Ligands ; Models, Molecular ; Crystallography, X-Ray
Czasopismo naukowe
Tytuł:
Towards the standardized presentation and publication of small-angle scattering data from biomolecules in solution.
Autorzy:
Czjzek M; Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, Bretagne France.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Feb 01; Vol. 79 (Pt 2), pp. 98-99. Date of Electronic Publication: 2023 Feb 07.
Typ publikacji:
Journal Article
MeSH Terms:
Scattering, Small Angle*
X-Ray Diffraction
Czasopismo naukowe
Tytuł:
Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy.
Autorzy:
Toelzer C; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, United Kingdom.
Gupta K; Imophoron Ltd, St Philips Central, Albert Road, Bristol BS2 0XJ, United Kingdom.
Berger I; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, United Kingdom.
Schaffitzel C; School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, United Kingdom.
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Źródło:
Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Feb 01; Vol. 79 (Pt 2), pp. 111-121. Date of Electronic Publication: 2023 Jan 20.
Typ publikacji:
Journal Article
MeSH Terms:
Antiviral Agents*/metabolism
Antiviral Agents*/pharmacology
COVID-19*/therapy
COVID-19*/virology
Cryoelectron Microscopy*
Linoleic Acid*/metabolism
Linoleic Acid*/pharmacology
SARS-CoV-2*/drug effects
SARS-CoV-2*/metabolism
SARS-CoV-2*/ultrastructure
Humans ; Communicable Disease Control ; Pandemics ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/ultrastructure
SCR Organism:
SARS-CoV-2 variants
Czasopismo naukowe

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