Secondary Structure in Free and Assisted Modeling of Proteins with the Coarse-Grained UNRES Force Field.

Autor: Lubecka EA; Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland., Czaplewski C; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Gdańsk, Poland., Sieradzan AK; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Gdańsk, Poland., Lipska AG; Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk, Poland., Dziadek Ł; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Gdańsk, Poland., Liwo A; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, Gdańsk, Poland. adam.liwo@ug.edu.pl.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2025; Vol. 2867, pp. 19-41.

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.

Autor: Lensink MF; University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Brysbaert G; University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Nadzirin N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Velankar S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Chaleil RAG; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Gerguri T; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Bates PA; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Laine E; CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France., Carbone A; CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, Paris, France.; Institut Universitaire de France (IUF), Paris, France., Grudinin S; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France., Kong R; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Liu RR; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Xu XM; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Shi H; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Chang S; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Eisenstein M; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel., Karczynska A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Czaplewski C; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Lubecka E; Institute of Informatics, Faculty of Mathematics, Physics, and Informatics, University of Gdańsk, Gdańsk, Poland., Lipska A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Krupa P; Polish Academy of Sciences, Institute of Physics, Warsaw, Poland., Mozolewska M; Polish Academy of Sciences, Institute of Computer Science, Warsaw, Poland., Golon Ł; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Samsonov S; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Liwo A; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea., Crivelli S; Department of Computer Science, UC Davis, Davis, California., Pagès G; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France., Karasikov M; Department of Computer Science, ETH, Zurich, Switzerland., Kadukova M; Université Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, Grenoble, France.; Moscow Institute of Physics and Technology, Dolgoprudniy, Russia., Yan Y; School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China., Huang SY; School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, China., Rosell M; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain., Rodríguez-Lumbreras LA; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain., Romero-Durana M; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Díaz-Bueno L; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Fernandez-Recio J; Barcelona Supercomputing Center (BSC), Barcelona, Spain.; Instituto de Ciencias de la Vid y del Vino (ICVV-CSIC), Logroño, Spain.; Instituto de Biología Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain., Christoffer C; Department of Computer Science, Purdue University, West Lafayette, Indiana., Terashi G; Department of Biological Sciences, Purdue University, West Lafayette, Indiana., Shin WH; Department of Biological Sciences, Purdue University, West Lafayette, Indiana., Aderinwale T; Department of Computer Science, Purdue University, West Lafayette, Indiana., Maddhuri Venkata Subraman SR; Department of Computer Science, Purdue University, West Lafayette, Indiana., Kihara D; Department of Computer Science, Purdue University, West Lafayette, Indiana., Kozakov D; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Vajda S; Department of Biomedical Engineering, Boston University, Boston, Massachusetts.; Department of Chemistry, Boston University, Boston, Massachusetts., Porter K; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Padhorny D; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Desta I; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Beglov D; Department of Biomedical Engineering, Boston University, Boston, Massachusetts., Ignatov M; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Kotelnikov S; Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York., Moal IH; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK., Ritchie DW; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Chauvot de Beauchêne I; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Maigret B; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Devignes MD; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Ruiz Echartea ME; University of Lorraine, CNRS, Inria, LORIA, Nancy, France., Barradas-Bautista D; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Cao Z; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Cavallo L; Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia., Oliva R; Department of Sciences and Technologies, University of Naples 'Parthenope', Napoli, Italy., Cao Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas., Shen Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas., Baek M; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Park T; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Woo H; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Seok C; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Braitbard M; Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel., Bitton L; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Scheidman-Duhovny D; Department of Biological Chemistry, Institute of Live Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Dapkūnas J; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Olechnovič K; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Venclovas Č; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Kundrotas PJ; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Belkin S; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Chakravarty D; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Badal VD; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Vakser IA; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas., Vreven T; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Vangaveti S; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Borrman T; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Weng Z; Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts., Guest JD; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Gowthaman R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Pierce BG; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland., Xu X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Duan R; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Qiu L; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri., Hou J; Department of Computer Science, University of Missouri, Columbia, Missouri., Ryan Merideth B; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri., Ma Z; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Department of Physics and Astronomy, University of Missouri, Columbia, Missouri., Cheng J; Department of Computer Science, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri., Zou X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri.; Informatics Institute, University of Missouri, Columbia, Missouri.; Department of Physics and Astronomy, University of Missouri, Columbia, Missouri.; Department of Biochemistry, University of Missouri, Columbia, Missouri., Koukos PI; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Roel-Touris J; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Ambrosetti F; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Geng C; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Schaarschmidt J; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Trellet ME; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Melquiond ASJ; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Xue L; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Jiménez-García B; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., van Noort CW; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Honorato RV; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Bonvin AMJJ; Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Wodak SJ; VIB Structural Biology Research Center, VUB, Brussels, Belgium.

Publikováno v: Proteins [Proteins] 2019 Dec; Vol. 87 (12), pp. 1200-1221. Date of Electronic Publication: 2019 Oct 25.

Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing.

Autor: Sieradzan AK; Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland. adams86@wp.pl., Golon Ł, Liwo A

Publikováno v: Physical chemistry chemical physics : PCCP [Phys Chem Chem Phys] 2018 Jul 25; Vol. 20 (29), pp. 19656-19663.

ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures.

Autor: Shi, Ya-Zhou¹ (AUTHOR) yzshi@wtu.edu.cn, Wu, Hao¹ (AUTHOR) 2115173008@mail.wtu.edu.cn, Li, Sha-Sha¹ (AUTHOR) 2315173010@mail.wtu.edu.cn, Li, Hui-Zhen¹ (AUTHOR) hzli@wtu.edu.cn, Zhang, Ben-Gong¹ (AUTHOR) yltan@wtu.edu.cn, Tan, Ya-Lan^1,2 (AUTHOR) yltan@wtu.edu.cn

Publikováno v: Molecules. Mar2024, Vol. 29 Issue 6, p1244. 13p.

The radiosensitivity of 5- and 6-bromocytidine derivatives--electron induced DNA degradation.

Autor: Chomicz L; Department of Chemistry, University of Gdansk, 80-308 Gdansk, Poland. janusz.rak@ug.edu.pl., Golon Ł, Rak J

Publikováno v: Physical chemistry chemical physics : PCCP [Phys Chem Chem Phys] 2014 Sep 28; Vol. 16 (36), pp. 19424-8.