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.

Accurate Boundary Integral Formulations for the Calculation of Electrostatic Forces with an Implicit-Solvent Model.

Autor: Addison-Smith I; Department of Mechanical Engineering, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile., Guzman HV; Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.; Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain., Cooper CD; Department of Mechanical Engineering, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile.; Centro Científico Tecnológico de Valparaíso, Universidad Técnica Federico Santa María, 2390123 Valparaíso, Chile.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2023 May 23; Vol. 19 (10), pp. 2996-3006. Date of Electronic Publication: 2023 Apr 27.

Single-chain models illustrate the 3D RNA folding shape during translation.

Autor: Guo T; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California., Modi OL; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California., Hirano J; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California., Guzman HV; Department of Theoretical Physics, Jozef Stefan Institute, Ljubljana, Slovenia., Tsuboi T; Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, Guangdong, China.

Publikováno v: Biophysical reports [Biophys Rep (N Y)] 2022 Aug 05; Vol. 2 (3), pp. 100065. Date of Electronic Publication: 2022 Aug 05 (Print Publication: 2022).

Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations.

Autor: Moreira RA; Soft Matter and Biosystems, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland., Baker JL; Department of Chemistry, The College of New Jersey, Ewing, NJ, USA., Guzman HV; Jožef Stefan Institute, Ljubljana, Slovenia., Poma AB; Soft Matter and Biosystems, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland. apoma@ippt.pan.pl.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2022; Vol. 2340, pp. 357-378.

Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models.

Autor: Poblete S; Instituto de Ciencias Físicas y Matemáticas, Universidad Austral de Chile, Valdivia 5091000, Chile.; Chile and Computational Biology Lab, Fundación Ciencia & Vida, Santiago 7780272, Chile., Guzman HV; Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia.

Publikováno v: Viruses [Viruses] 2021 Aug 06; Vol. 13 (8). Date of Electronic Publication: 2021 Aug 06.