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.

Explicit solvent repulsive scaling replica exchange molecular dynamics (RS-REMD) in molecular modeling of protein-glycosaminoglycan complexes.

Autor: Marcisz M; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.; Intercollegiate Faculty of Biotechnology, Universuty of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland., Gaardløs M; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland., Bojarski KK; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.; Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk, Poland., Siebenmorgen T; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany., Zacharias M; Physics Department, Technical University of Munich, Garching, Germany., Samsonov SA; Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.

Publikováno v: Journal of computational chemistry [J Comput Chem] 2022 Sep 15; Vol. 43 (24), pp. 1633-1640. Date of Electronic Publication: 2022 Jul 07.

Modulation of the expression and activity of cathepsin S in reconstructed human skin by neohesperidin dihydrochalcone.

Autor: Sage J; LVMH-Recherche, F-45800 Saint Jean de Braye, France., Renault J; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires, Team Mécanismes Protéolytiques dans l'Inflammation, F-37032 Tours, France., Domain R; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires, Team Mécanismes Protéolytiques dans l'Inflammation, F-37032 Tours, France., Bojarski KK; Faculty of Chemistry, University of Gdańsk, Gdańsk 80-308, Poland., Chazeirat T; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires, Team Mécanismes Protéolytiques dans l'Inflammation, F-37032 Tours, France., Saidi A; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires, Team Mécanismes Protéolytiques dans l'Inflammation, F-37032 Tours, France., Leblanc E; LVMH-Recherche, F-45800 Saint Jean de Braye, France., Nizard C; LVMH-Recherche, F-45800 Saint Jean de Braye, France., Samsonov SA; Faculty of Chemistry, University of Gdańsk, Gdańsk 80-308, Poland., Kurfurst R; LVMH-Recherche, F-45800 Saint Jean de Braye, France., Lalmanach G; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires, Team Mécanismes Protéolytiques dans l'Inflammation, F-37032 Tours, France., Lecaille F; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires, Team Mécanismes Protéolytiques dans l'Inflammation, F-37032 Tours, France. Electronic address: fabien.lecaille@univ-tours.fr.

Publikováno v: Matrix biology : journal of the International Society for Matrix Biology [Matrix Biol] 2022 Mar; Vol. 107, pp. 97-112. Date of Electronic Publication: 2022 Feb 12.

The abnormal accumulation of heparan sulfate in patients with mucopolysaccharidosis prevents the elastolytic activity of cathepsin V.

Autor: Chazeirat T; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team 'Mécanismes Protéolytiques Dans l'Inflammation', Tours, France. Electronic address: thibault.chazeirat@etu.univ-tours.fr., Denamur S; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team 'Mécanismes Protéolytiques Dans l'Inflammation', Tours, France; Pediatric Department, Reference Center for Inborn Errors of Metabolism ToTeM, CHRU Tours, France. Electronic address: sophie.denamur@gmail.com., Bojarski KK; Faculty of Chemistry, University of Gdańsk, Poland. Electronic address: krzysztof.bojarski@ug.edu.pl., Andrault PM; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address: andrault_pm@yahoo.fr., Sizaret D; Anatomical Pathology and Cytology Department, Bretonneau Hospital, CHRU Tours, France. Electronic address: D.SIZARET@chu-tours.fr., Zhang F; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA. Electronic address: zhangf2@rpi.edu., Saidi A; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team 'Mécanismes Protéolytiques Dans l'Inflammation', Tours, France. Electronic address: ahlame.saidi@univ-tours.fr., Tardieu M; Pediatric Department, Reference Center for Inborn Errors of Metabolism ToTeM, CHRU Tours, France. Electronic address: M.TARDIEU@chu-tours.fr., Linhardt RJ; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA. Electronic address: linhar@rpi.edu., Labarthe F; Pediatric Department, Reference Center for Inborn Errors of Metabolism ToTeM, CHRU Tours, France; INSERM, UMR 1069, Nutrition, Croissance et Cancer (N2C), Tours, France. Electronic address: francois.labarthe@univ-tours.fr., Brömme D; Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address: dbromme@dentistry.ubc.ca., Samsonov SA; Faculty of Chemistry, University of Gdańsk, Poland. Electronic address: sergey.samsonov@ug.edu.pl., Lalmanach G; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team 'Mécanismes Protéolytiques Dans l'Inflammation', Tours, France. Electronic address: gilles.lalmanach@univ-tours.fr., Lecaille F; Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team 'Mécanismes Protéolytiques Dans l'Inflammation', Tours, France. Electronic address: fabien.lecaille@univ-tours.fr.

Publikováno v: Carbohydrate polymers [Carbohydr Polym] 2021 Feb 01; Vol. 253, pp. 117261. Date of Electronic Publication: 2020 Oct 20.

Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study.

Autor: Bojarski KK; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland., Karczyńska AS; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland., Samsonov SA; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2020 Apr 27; Vol. 60 (4), pp. 2247-2256. Date of Electronic Publication: 2020 Apr 01.