Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution.

Autor: Dziadek ŁJ; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland., Sieradzan AK; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland., Czaplewski C; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland.; School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 02455, Republic of Korea., Zalewski M; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland., Banaś F; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland., Toczek M; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland., Nisterenko W; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland., Grudinin S; LJK, University Grenoble Alpes, CNRS, Grenoble INP, F-38000 Grenoble, France., Liwo A; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland., Giełdoń A; Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2024 Sep 10; Vol. 20 (17), pp. 7667-7681. Date of Electronic Publication: 2024 Aug 22.

Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.

Autor: Rogoża NH; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Bażyńskiego 8, 80-309 Gdańsk, Poland., Krupa MA; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Bażyńskiego 8, 80-309 Gdańsk, Poland., Krupa P; Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland., Sieradzan AK; Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Bażyńskiego 8, 80-309 Gdańsk, Poland.

Publikováno v: Molecules (Basel, Switzerland) [Molecules] 2024 Apr 23; Vol. 29 (9). Date of Electronic Publication: 2024 Apr 23.

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

Autor: Lensink MF; Univ. Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Brysbaert G; Univ. Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Raouraoua N; Univ. Lille, CNRS, UMR8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France., Bates PA; Biomolecular Modeling Laboratory, The Francis Crick Institute, London, UK., Giulini M; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands., Honorato RV; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands., van Noort C; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands., Teixeira JMC; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands., Bonvin AMJJ; Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands., Kong R; 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., Liu J; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Guo Z; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Chen X; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Morehead A; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Roy RS; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Wu T; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Giri N; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Quadir F; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Chen C; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Cheng J; Dept. of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA., Del Carpio CA; Choju-Medical Institute, Fukushimuta Hospital, Toyohashi-City, Aichi-ken, Japan., Ichiishi E; International University of Health and Welfare (IUHV Hospital), Nasushiobara-City, Japan., Rodriguez-Lumbreras LA; Instituto de Ciencias de la Vida 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 Vida y del Vino (ICVV), CSIC - Universidad de La Rioja - Gobierno de La Rioja, Logrono, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Harmalkar A; Dept. of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA., Chu LS; Dept. of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA., Canner S; Dept. of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA., Smanta R; Dept. of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA., Gray JJ; Dept. of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA.; Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, USA., 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., He J; School of Physics, Huazhong University of Science and Technology, Wuhan, China., Tao H; School of Physics, Huazhong University of Science and Technology, Wuhan, China., Huang SY; School of Physics, Huazhong University of Science and Technology, Wuhan, China., Roel-Touris J; Protein Design and Modeling Lab, Dept. of Structural Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain., Jimenez-Garcia B; Zymvol Biomodeling, Barcelona, Spain., Christoffer CW; Dept. of Computer Science, Purdue University, West Lafayette, Indiana, USA., Jain AJ; Dept. of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Kagaya Y; Dept. of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Kannan H; Dept. of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.; Dept. of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India., Nakamura T; Dept. of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Terashi G; Dept. of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Verburgt JC; Dept. of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Zhang Y; Dept. of Computer Science, Purdue University, West Lafayette, Indiana, USA., Zhang Z; Dept. of Computer Science, Purdue University, West Lafayette, Indiana, USA., Fujuta H; Dept. of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India., Sekijima M; Dept. of Computer Science, Tokyo Institute of Technology, Yokohama, Japan., Kihara D; Dept. of Computer Science, Purdue University, West Lafayette, Indiana, USA.; Dept. of Biological Sciences, Purdue University, West Lafayette, Indiana, USA., Khan O; Boston University, Boston, Massachusetts, USA., Kotelnikov S; Stony Brook University, New York City, New York, USA., Ghani U; Boston University, Boston, Massachusetts, USA., Padhorny D; Stony Brook University, New York City, New York, USA., Beglov D; Boston University, Boston, Massachusetts, USA., Vajda S; Boston University, Boston, Massachusetts, USA., Kozakov D; Stony Brook University, New York City, New York, USA., Negi SS; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA., Ricciardelli T; King Abdullah University of Science and Technology (KAUST), Saudi Arabia., Barradas-Bautista D; King Abdullah University of Science and Technology (KAUST), Saudi Arabia., Cao Z; King Abdullah University of Science and Technology (KAUST), Saudi Arabia., Chawla M; King Abdullah University of Science and Technology (KAUST), Saudi Arabia., Cavallo L; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.; Department of Chemistry and Biology, University of Salerno, Fisciano, Italy., Oliva R; University of Naples 'Parthenope', Naples, Italy., Yin R; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA., Cheung M; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Dept. of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA., Guest JD; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA., Lee J; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA., Pierce BG; University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA.; Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA., Shor B; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Cohen T; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Halfon M; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Schneidman-Duhovny D; School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel., Zhu S; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA., Yin R; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA., Sun Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA., Shen Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, USA.; Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA.; Institute of Biosciences and Technology and Department of Translational Medical Sciences, Texas A&M University, Houston, Texas, USA., Maszota-Zieleniak M; University of Gdansk, Gdansk, Poland., Bojarski KK; Technical University of Gdansk, Gdansk, Poland., Lubecka EA; Technical University of Gdansk, Gdansk, Poland., Marcisz M; University of Gdansk, Gdansk, Poland., Danielsson A; University of Gdansk, Gdansk, Poland., Dziadek L; University of Gdansk, Gdansk, Poland., Gaardlos M; University of Gdansk, Gdansk, Poland., Gieldon A; University of Gdansk, Gdansk, Poland., Liwo A; University of Gdansk, Gdansk, Poland., Samsonov SA; University of Gdansk, Gdansk, Poland., Slusarz R; University of Gdansk, Gdansk, Poland., Zieba K; University of Gdansk, Gdansk, Poland., Sieradzan AK; University of Gdansk, Gdansk, Poland., Czaplewski C; University of Gdansk, Gdansk, Poland., Kobayashi S; School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan., Miyakawa Y; School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan., Kiyota Y; School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan., Takeda-Shitaka M; School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan., Olechnovic K; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Valancauskas L; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Dapkunas J; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Venclovas C; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania., Wallner B; Bioinformatics Division, Department of Physics, Chemistry, and Biology, Linkoping University, Linköping, Sweden., Yang L; National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin, China.; School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, New South Wales, Australia., Hou C; School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin, China., He X; National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin, China.; Shenzhen STRONG Advanced Materials Research Institute Col, Ltd, Shenzhen, People's Republic of China., Guo S; National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin, China., Jiang S; National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin, China., Ma X; National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin, China., Duan R; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA., Qui L; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA., Xu X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA., Zou X; Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri, USA.; Dept. of Physics and Astronomy, University of Missouri, Columbia, Missouri, USA.; Dept. of Biochemistry, University of Missouri, Columbia, Missouri, USA.; Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA., Velankar S; Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK., Wodak SJ; VIB-VUB Center for Structural Biology, Brussels, Belgium.

Publikováno v: Proteins [Proteins] 2023 Dec; Vol. 91 (12), pp. 1658-1683. Date of Electronic Publication: 2023 Oct 31.

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.

Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin.

Autor: Danielsson A; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland., Samsonov SA; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland., Liwo A; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland., Sieradzan AK; Faculty of Chemistry, University of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.

Publikováno v: Journal of chemical theory and computation [J Chem Theory Comput] 2023 Sep 12; Vol. 19 (17), pp. 6023-6036. Date of Electronic Publication: 2023 Aug 16.