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.

Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches.

Autor: Lipska AG; Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland., Sieradzan AK; Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland.; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland., Atmaca S; Kocaeli University, Institute of Science, Umuttepe Yerleşkesi, 41001 İzmit/Kocaeli̇, Türkiye., Czaplewski C; Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland.; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland., Liwo A; Centre of Informatics Tri-city Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland.; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.

Publikováno v: The journal of physical chemistry letters [J Phys Chem Lett] 2023 Nov 09; Vol. 14 (44), pp. 9824-9833. Date of Electronic Publication: 2023 Oct 27.

UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales.

Autor: Ocetkiewicz KM; Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland., Czaplewski C; Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland.; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-309, Poland., Krawczyk H; Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland.; Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland., Lipska AG; Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland., Liwo A; Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland.; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-309, Poland., Proficz J; Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland., Sieradzan AK; Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland.; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-309, Poland., Czarnul P; Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk, Gdańsk 80-233, Poland.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2023 Jun 01; Vol. 39 (6).

Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins.

Autor: Lipska AG; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland. lipska.ag@gmail.com., Antoniak AM; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland., Wesołowski P; Intercollegiate Faculty of Biotechnology of UG i MUG, Abrahama 58, 80-307, Gdańsk, Poland., Warszawski A; Intercollegiate Faculty of Biotechnology of UG i MUG, Abrahama 58, 80-307, Gdańsk, Poland., Samsonov SA; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland., Sieradzan AK; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.

Publikováno v: Journal of molecular modeling [J Mol Model] 2022 Jun 24; Vol. 28 (7), pp. 201. Date of Electronic Publication: 2022 Jun 24.

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

Autor: Lensink MF; CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France., Brysbaert G; CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France., Mauri T; CNRS UMR8576 UGSF, Institute for Structural and Functional Glycobiology, University of Lille, Lille, France., Nadzirin N; Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Velankar S; Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK., Chaleil RAG; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Clarence T; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Bates PA; Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK., Kong R; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Liu B; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Yang G; Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China., Liu M; 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., Lu X; 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., Roy RS; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Quadir F; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Liu J; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Cheng J; Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.; Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA., Antoniak A; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Czaplewski C; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Giełdoń A; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Kogut M; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Lipska AG; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Liwo A; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Lubecka EA; Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, Gdansk, Poland., Maszota-Zieleniak M; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Sieradzan AK; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Ślusarz R; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Wesołowski PA; Faculty of Chemistry, University of Gdansk, Gdansk, Poland.; Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland., Zięba K; Faculty of Chemistry, University of Gdansk, Gdansk, Poland., Del Carpio Muñoz CA; Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan., Ichiishi E; International University of Health and Welfare Hospital (IUHW Hospital), Nasushiobara City, Japan., Harmalkar A; Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA., Gray JJ; Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA., Bonvin AMJJ; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Ambrosetti F; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Vargas Honorato R; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Jandova Z; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Jiménez-García B; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Koukos PI; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Van Keulen S; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Van Noort CW; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Réau M; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Roel-Touris J; Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands., Kotelnikov S; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.; Innopolis University, Russia., Padhorny D; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA., Porter KA; Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA., Alekseenko A; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.; Institute of Computer-Aided Design of the Russian Academy of Sciences, Moscow, Russia., Ignatov M; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA., Desta I; Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA., Ashizawa R; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA., Sun Z; Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA., Ghani U; Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA., Hashemi N; Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA., Vajda S; Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.; Department of Chemistry, Boston University, Boston, Massachusetts, USA., Kozakov D; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA., Rosell M; Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Rodríguez-Lumbreras LA; Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Fernandez-Recio J; Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de la Rioja - Gobierno de La Rioja, Logrono, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Karczynska A; Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France., Grudinin S; Université Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France., Yan Y; School of Physics, Huazhong University of Science and Technology, Wuhan, China., Li H; School of Physics, Huazhong University of Science and Technology, Wuhan, China., Lin P; School of Physics, Huazhong University of Science and Technology, Wuhan, China., Huang SY; School of Physics, Huazhong University of Science and Technology, Wuhan, China., Christoffer C; Department of Computer Science, Purdue University, West Lafayette, Indiana, USA., Terashi G; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Verburgt J; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Sarkar D; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Aderinwale T; Department of Computer Science, Purdue University, West Lafayette, Indiana, USA., Wang X; Department of Computer Science, Purdue University, West Lafayette, Indiana, USA., Kihara D; Department of Computer Science, Purdue University, West Lafayette, Indiana, USA.; Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Nakamura T; Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan., Hanazono Y; Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki, Japan., Gowthaman R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA., Guest JD; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA., Yin R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA., Taherzadeh G; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA., Pierce BG; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, Maryland, USA., Barradas-Bautista D; King Abdullah University of Science and Technology, Thuwal, Saudi Arabia., Cao Z; King Abdullah University of Science and Technology, Thuwal, Saudi Arabia., Cavallo L; King Abdullah University of Science and Technology, Thuwal, Saudi Arabia., Oliva R; University of Naples 'Parthenope', Napoli, Italy., Sun Y; Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA., Zhu S; Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA., Shen Y; Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA., Park T; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Woo H; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Yang J; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Kwon S; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Won J; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Seok C; Department of Chemistry, Seoul National University, Seoul, Republic of Korea., Kiyota Y; School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan., Kobayashi S; School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan., Harada Y; School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan., Takeda-Shitaka M; School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan., Kundrotas PJ; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA., Singh A; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA., Vakser IA; Computational Biology Program and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA., 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., Duan R; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA., Qiu L; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA., Xu X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA., Zhang S; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA., Zou X; Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA.; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA.; Department of Physics and Astronomy, University of Missouri, Columbia, Missouri, USA.; Department of Biochemistry, University of Missouri, Columbia, Missouri, USA., Wodak SJ; Center for Structural Biology, VIB-VUB, Brussels, Belgium.

Publikováno v: Proteins [Proteins] 2021 Dec; Vol. 89 (12), pp. 1800-1823. Date of Electronic Publication: 2021 Sep 13.