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The CCP4 suite: integrative software for macromolecular crystallography.

Autor: Agirre J; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Atanasova M; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Bagdonas H; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Ballard CB; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Baslé A; Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom., Beilsten-Edmands J; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Borges RJ; The Center of Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Av. Dr. André Tosello 550, 13083-886 Campinas, Brazil., Brown DG; Laboratoires Servier SAS Institut de Recherches, Croissy-sur-Seine, France., Burgos-Mármol JJ; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom., Berrisford JM; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom., Bond PS; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Caballero I; Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain., Catapano L; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom., Chojnowski G; European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany., Cook AG; The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, The King's Buildings, Edinburgh EH9 3BF, United Kingdom., Cowtan KD; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Croll TI; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom., Debreczeni JÉ; Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, United Kingdom., Devenish NE; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Dodson EJ; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Drevon TR; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Emsley P; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom., Evans G; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Evans PR; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom., Fando M; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Foadi J; Department of Mathematical Sciences, University of Bath, Bath, United Kingdom., Fuentes-Montero L; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Garman EF; Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, United Kingdom., Gerstel M; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Gildea RJ; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Hatti K; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom., Hekkelman ML; Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands., Heuser P; European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany., Hoh SW; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Hough MA; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Jenkins HT; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Jiménez E; Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain., Joosten RP; Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands., Keegan RM; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Keep N; Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom., Krissinel EB; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Kolenko P; Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Břehová 7, 115 19 Prague 1, Czech Republic., Kovalevskiy O; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Lamzin VS; European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany., Lawson DM; Department of Biochemistry and Metabolism, John Innes Centre, Norwich NR4 7UH, United Kingdom., Lebedev AA; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Leslie AGW; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom., Lohkamp B; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden., Long F; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom., Malý M; Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom., McCoy AJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom., McNicholas SJ; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Medina A; Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain., Millán C; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom., Murray JW; Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom., Murshudov GN; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom., Nicholls RA; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom., Noble MEM; Translational and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom., Oeffner R; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom., Pannu NS; Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands., Parkhurst JM; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Pearce N; Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden., Pereira J; Biozentrum and SIB Swiss Institute of Bioinformatics, University of Basel, 4056 Basel, Switzerland., Perrakis A; Oncode Institute and Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands., Powell HR; Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom., Read RJ; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom., Rigden DJ; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom., Rochira W; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Sammito M; Discovery Centre, Biologics Engineering, AstraZeneca, Biomedical Campus, 1 Francis Crick Avenue, Trumpington, Cambridge CB2 0AA, United Kingdom., Sánchez Rodríguez F; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Sheldrick GM; Department of Structural Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 4, 37077 Göttingen, Germany., Shelley KL; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA., Simkovic F; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom., Simpkin AJ; Laboratoires Servier SAS Institut de Recherches, Croissy-sur-Seine, France., Skubak P; Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands., Sobolev E; European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany., Steiner RA; Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom., Stevenson K; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Tews I; Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom., Thomas JMH; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom., Thorn A; Institute for Nanostructure and Solid State Physics, Universität Hamburg, 22761 Hamburg, Germany., Valls JT; Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain., Uski V; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Usón I; Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB-CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain., Vagin A; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Velankar S; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom., Vollmar M; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom., Walden H; School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom., Waterman D; STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom., Wilson KS; York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom., Winn MD; Scientific Computing Department, Science and Technology Facilities Council, Didcot OX11 0FA, United Kingdom., Winter G; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom., Wojdyr M; Global Phasing Limited (United Kingdom), Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom., Yamashita K; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.

Publikováno v: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2023 Jun 01; Vol. 79 (Pt 6), pp. 449-461. Date of Electronic Publication: 2023 May 30.

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.

Autor: Varadi M; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK., Nair S; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK., Sillitoe I; Department of Structural and Molecular Biology, UCL, London WC1E 6BT, UK., Tauriello G; Biozentrum, University of Basel, Basel 4056, Switzerland.; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland., Anyango S; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK., Bienert S; Biozentrum, University of Basel, Basel 4056, Switzerland.; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland., Borges C; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.; European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany., Deshpande M; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK., Green T; DeepMind, London EC4A 3TW, UK., Hassabis D; DeepMind, London EC4A 3TW, UK., Hatos A; Department of Biomedical Sciences, University of Padova, Padova 35129, Italy.; Department of Oncology, Lausanne University Hospital, Lausanne 1015, Switzerland.; Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.; Swiss Cancer Center Leman, Lausanne 1005, Switzerland., Hegedus T; Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary., Hekkelman ML; Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands., Joosten R; Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands., Jumper J; DeepMind, London EC4A 3TW, UK., Laydon A; DeepMind, London EC4A 3TW, UK., Molodenskiy D; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.; European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany., Piovesan D; Department of Biomedical Sciences, University of Padova, Padova 35129, Italy., Salladini E; Department of Biomedical Sciences, University of Padova, Padova 35129, Italy., Salzberg SL; Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA., Sommer MJ; Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA., Steinegger M; School of Biology, Seoul National University, Seoul 82-2-880-6971, 6977, South Korea., Suhajda E; Department of Biophysics and Radiation Biology, Semmelweis University, Budapest 1094, Hungary., Svergun D; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.; European Molecular Biology Laboratory, EMBL Hamburg, Hamburg 69117, Germany., Tenorio-Ku L; Department of Biomedical Sciences, University of Padova, Padova 35129, Italy., Tosatto S; Department of Biomedical Sciences, University of Padova, Padova 35129, Italy., Tunyasuvunakool K; DeepMind, London EC4A 3TW, UK., Waterhouse AM; Biozentrum, University of Basel, Basel 4056, Switzerland.; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland., Žídek A; DeepMind, London EC4A 3TW, UK., Schwede T; Biozentrum, University of Basel, Basel 4056, Switzerland.; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland., Orengo C; Department of Structural and Molecular Biology, UCL, London WC1E 6BT, UK., Velankar S; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton CB10 1SA, UK.

Publikováno v: GigaScience [Gigascience] 2022 Nov 30; Vol. 11.

New restraints and validation approaches for nucleic acid structures in PDB-REDO.

Autor: de Vries I; Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands., Kwakman T; Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands., Lu XJ; Department of Biological Sciences, Columbia University, New York, NY 10027, USA., Hekkelman ML; Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands., Deshpande M; Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom., Velankar S; Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom., Perrakis A; Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands., Joosten RP; Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

Publikováno v: Acta crystallographica. Section D, Structural biology [Acta Crystallogr D Struct Biol] 2021 Sep 01; Vol. 77 (Pt 9), pp. 1127-1141. Date of Electronic Publication: 2021 Aug 24.

A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry.

Autor: Sobolev OV; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: osobolev@lbl.gov., Afonine PV; 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., Hekkelman ML; Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands., Joosten RP; Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands. Electronic address: r.joosten@nki.nl., Perrakis A; Division of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands., Adams PD; Molecular Biosciences and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA.

Publikováno v: Structure (London, England : 1993) [Structure] 2020 Nov 03; Vol. 28 (11), pp. 1249-1258.e2. Date of Electronic Publication: 2020 Aug 27.