RNA-Puzzles Round V: blind predictions of 23 RNA structures.

Autor: Bu F; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China., Adam Y; Inter-institutional Graduate Program on Bioinformatics, Department of Computer Science and Mathematics, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil.; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria., Adamiak RW; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.; Institute of Computing Science, Poznan University of Technology, Poznan, Poland., Antczak M; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.; Institute of Computing Science, Poznan University of Technology, Poznan, Poland., de Aquino BRH; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Badepally NG; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Batey RT; Department of Biochemistry, University of Colorado at Boulder, Boulder, CO, USA., Baulin EF; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Boinski P; Institute of Computing Science, Poznan University of Technology, Poznan, Poland., Boniecki MJ; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Bujnicki JM; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Carpenter KA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA., Chacon J; Department of Biochemistry, Stanford University, Stanford, CA, USA.; Department of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA., Chen SJ; Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA., Chiu W; Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, USA., Cordero P; Department of Biochemistry, Stanford University, Stanford, CA, USA.; Stripe, South San Francisco, CA, USA., Das NK; Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA., Das R; Department of Biochemistry, Stanford University, Stanford, CA, USA.; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.; Biophysics program, Stanford University, Stanford, CA, USA., Dawson WK; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., DiMaio F; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Ding F; Department of Physics and Astronomy, Clemson University, Clemson, SC, USA., Dock-Bregeon AC; Laboratory of Integrative Biology of Marine Models (LBI2M), Sorbonne University-CNRS UMR8227, Roscoff, France., Dokholyan NV; Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA., Dror RO; Department of Computer Science, Stanford University, Stanford, CA, USA.; Department of Structural Biology, Stanford University, Stanford, CA, USA.; Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA., Dunin-Horkawicz S; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Eismann S; Department of Applied Physics, Stanford University, Stanford, CA, USA.; Atomic AI, South San Francisco, CA, USA., Ennifar E; Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France., Esmaeeli R; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Farsani MA; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Ferré-D'Amaré AR; Laboratory of Nucleic Acids, National Heart, Lung and Blood Institute, Bethesda, MD, USA., Geniesse C; Department of Biochemistry, Stanford University, Stanford, CA, USA.; Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Ghanim GE; Medical Research Council Laboratory of Molecular Biology, Cambridge, UK., Guzman HV; Instituto de Ciencia de Materials de Barcelona, ICMAB-CSIC, Bellaterra E-08193, Spain & Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain., Hood IV; Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA., Huang L; Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University Guangzhou, Guangdong, China., Jain DS; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Jaryani F; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Jin L; Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA., Joshi A; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Karelina M; Biophysics program, Stanford University, Stanford, CA, USA.; Department of Computer Science, Stanford University, Stanford, CA, USA., Kieft JS; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA.; New York Structural Biology Center, New York, NY, USA., Kladwang W; Department of Biochemistry, Stanford University, Stanford, CA, USA.; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA., Kmiecik S; Laboratory of Computational Biology, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland., Koirala D; Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA., Kollmann M; Department of Computer Science, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany., Kretsch RC; Biophysics program, Stanford University, Stanford, CA, USA., Kurciński M; Laboratory of Computational Biology, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland., Li J; Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA., Li S; Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA., Magnus M; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA., Masquida B; UMR 7156, CNRS - Université de Strasbourg, IPCB, Strasbourg, France., Moafinejad SN; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Mondal A; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Mukherjee S; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Nguyen THD; Medical Research Council Laboratory of Molecular Biology, Cambridge, UK., Nikolaev G; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Nithin C; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.; Laboratory of Computational Biology, Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Warsaw, Poland., Nye G; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA., Pandaranadar Jeyeram IPN; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Perez A; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Pham P; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA., Piccirilli JA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.; Department of Chemistry, The University of Chicago, Chicago, IL, USA., Pilla SP; Laboratory of Computational Biology, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland., Pluta R; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Poblete S; Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago, Chile.; Centro BASAL Ciencia & Vida, Universidad San Sebastián, Santiago, Chile., Ponce-Salvatierra A; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Popenda M; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland., Popenda L; NanoBioMedical Centre, Adam Mickiewicz University, Poznan, Poland., Pucci F; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium., Rangan R; Biophysics program, Stanford University, Stanford, CA, USA.; Atomic AI, South San Francisco, CA, USA., Ray A; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Ren A; Life Sciences Institute, Zhejiang University, Hangzhou, China., Sarzynska J; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland., Sha CM; Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA., Stefaniak F; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Su Z; The State Key Laboratory of Biotherapy, West China Hospital, Chengdu, China., Suddala KC; Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA., Szachniuk M; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.; Institute of Computing Science, Poznan University of Technology, Poznan, Poland., Townshend R; Department of Computer Science, Stanford University, Stanford, CA, USA.; Atomic AI, South San Francisco, CA, USA., Trachman RJ 3rd; Laboratory of Nucleic Acids, National Heart, Lung and Blood Institute, Bethesda, MD, USA., Wang J; Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA., Wang W; MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China., Watkins A; Department of Biochemistry, Stanford University, Stanford, CA, USA.; Prescient Design, Genentech Research and Early Development, South San Francisco, CA, USA., Wirecki TK; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Xiao Y; School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China., Xiong P; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.; Department of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, China., Xiong Y; School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China., Yang J; MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China., Yesselman JD; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.; Department of Chemistry, University of Nebraska, Lincoln, NE, USA., Zhang J; Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA., Zhang Y; School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, China., Zhang Z; Department of Physics and Astronomy, Clemson University, Clemson, SC, USA., Zhou Y; Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA., Zok T; Institute of Computing Science, Poznan University of Technology, Poznan, Poland., Zhang D; Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA., Zhang S; Department of Physics, Department of Biochemistry and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA., Żyła A; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland., Westhof E; Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France. e.westhof@ibmc-cnrs.unistra.fr.; Engineering Research Center of Clinical Functional Materials and Diagnosis & Treatment Devices of Zhejiang Province, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China. e.westhof@ibmc-cnrs.unistra.fr., Miao Z; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China. miao_zhichao@gzlab.ac.cn.; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China. miao_zhichao@gzlab.ac.cn.; European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, UK. miao_zhichao@gzlab.ac.cn.

Publikováno v: Nature methods [Nat Methods] 2024 Dec 02. Date of Electronic Publication: 2024 Dec 02.

RNA dynamics from experimental and computational approaches.

Autor: Bussi G; Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy. Electronic address: bussi@sissa.it., Bonomi M; Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France. Electronic address: mbonomi@pasteur.fr., Gkeka P; Integrated Drug Discovery, Molecular Design Sciences, Sanofi, Vitry-sur-Seine, France. Electronic address: paraskevi.gkeka@sanofi.com., Sattler M; Technical University of Munich, Munich, Germany; Helmholtz Munich, Munich, Germany. Electronic address: michael.sattler@helmholtz-munich.de., Al-Hashimi HM; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA., Auffinger P; Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 2 Allée Konrad Roentgen, 67084 Strasbourg, France., Duca M; Université Côte d'Azur, CNRS, Institute of Chemistry of Nice, Nice, France., Foricher Y; Integrated Drug Discovery, Small Molecules Medicinal Chemistry, Sanofi, Vitry-sur-Seine, France., Incarnato D; Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands., Jones AN; Department of Chemistry, New York University, New York, NY, USA., Kirmizialtin S; Department of Chemistry, New York University, New York, NY, USA; Chemistry Program, Science Division, New York University, Abu Dhabi, United Arab Emirates., Krepl M; Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 00, Czech Republic., Orozco M; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, and Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain., Palermo G; Department of Bioengineering and Department of Chemistry, The University of California, Riverside, Riverside, CA, USA., Pasquali S; Laboratoire Biologie Fonctionnelle et Adaptative, CNRS UMR 8251 INSERM ERL 1133, Université Paris Cité, 35 rue Hélène Brion, 75013 Paris, France., Salmon L; Centre de RMN à Très Hauts Champs, UMR 5082 (CNRS, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1), University of Lyon, 69100 Villeurbanne, France., Schwalbe H; Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, 60438 Frankfurt/Main, Germany., Westhof E; Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67084 Strasbourg, France., Zacharias M; Physics Department and Center of Protein Assemblies, Technical University of Munich, Munich, Germany.

Publikováno v: Structure (London, England : 1993) [Structure] 2024 Sep 05; Vol. 32 (9), pp. 1281-1287.

Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons.

Autor: Kompatscher M; Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria., Bartosik K; Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria., Erharter K; Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria., Plangger R; Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria., Juen FS; Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria., Kreutz C; Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria., Micura R; Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria., Westhof E; Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l'ARN, CNRS UPR 9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France., Erlacher MD; Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2024 Feb 09; Vol. 52 (3), pp. 1374-1386.

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Corrigendum: Identification of U ^p 47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium.

Autor: Wolff P, Lechner A, Droogmans L, Grosjean H, Westhof E

Publikováno v: RNA (New York, N.Y.) [RNA] 2023 Dec; Vol. 29 (12), pp. 1973.