MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface.

Autor: Samarasinghe KW; SIB, Swiss Institute of Bioinformatics, Geneva, Switzerland., Kotlyar M; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada., Vallet SD; Institut de Biologie Structurale, UMR 5075, CEA, CNRS, Université Grenoble Alpes, Grenoble 38000, France., Hayes C; SIB, Swiss Institute of Bioinformatics, Geneva, Switzerland., Naba A; Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL 60612, USA., Jurisica I; Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada.; Departments of Medical Biophysics and Computer Science, and the Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia., Lisacek F; SIB, Swiss Institute of Bioinformatics, Geneva, Switzerland., Ricard-Blum S; Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), UMR 5246, CNRS, Université Lyon 1, Villeurbanne 69622, France.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2024 Nov 18. Date of Electronic Publication: 2024 Nov 18.

The IntAct database: efficient access to fine-grained molecular interaction data.

Autor: Del Toro N; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Shrivastava A; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Ragueneau E; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Meldal B; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Combe C; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK., Barrera E; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Perfetto L; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK.; Fondazione Human Technopole, Milan 20157, Italy., How K; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA., Ratan P; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA., Shirodkar G; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA., Lu O; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA., Mészáros B; Gibson Group, European Molecular Biology Laboratory, Heidelberg 69117, Germany., Watkins X; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Pundir S; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Licata L; Bioinformatics and Computational Biology Unit, Dept. of Molecular Biology, University of Rome Tor Vergata, Rome, Italy., Iannuccelli M; Bioinformatics and Computational Biology Unit, Dept. of Molecular Biology, University of Rome Tor Vergata, Rome, Italy., Pellegrini M; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA., Martin MJ; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Panni S; Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Rende, Italy., Duesbury M; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK.; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA., Vallet SD; ICBMS UMR CNRS 5246, University Lyon 1, Lyon, Villeurbanne 69622, France., Rappsilber J; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.; Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany., Ricard-Blum S; ICBMS UMR CNRS 5246, University Lyon 1, Lyon, Villeurbanne 69622, France., Cesareni G; Bioinformatics and Computational Biology Unit, Dept. of Molecular Biology, University of Rome Tor Vergata, Rome, Italy., Salwinski L; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA., Orchard S; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Porras P; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Panneerselvam K; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK., Hermjakob H; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, Cambridgeshire CB10 1SD, UK.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2022 Jan 07; Vol. 50 (D1), pp. D648-D653.

Building Protein-Protein and Protein-Glycosaminoglycan Interaction Networks Using MatrixDB, the Extracellular Matrix Interaction Database.

Autor: Berthollier C; Univ Lyon, University Lyon 1, CNRS, ICBMS, UMR 5246, F-69622, Villeurbanne, France., Vallet SD; Univ Lyon, University Lyon 1, CNRS, ICBMS, UMR 5246, F-69622, Villeurbanne, France., Deniaud M; Univ Lyon, University Lyon 1, CNRS, ICBMS, UMR 5246, F-69622, Villeurbanne, France., Clerc O; Univ Lyon, University Lyon 1, CNRS, ICBMS, UMR 5246, F-69622, Villeurbanne, France., Ricard-Blum S; Univ Lyon, University Lyon 1, CNRS, ICBMS, UMR 5246, F-69622, Villeurbanne, France.

Publikováno v: Current protocols [Curr Protoc] 2021 Apr; Vol. 1 (4), pp. e47.

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.

Autor: Lazar T; VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology, Brussels 1050, Belgium.; Structural Biology Brussels, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels 1050, Belgium., Martínez-Pérez E; Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina.; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany., Quaglia F; Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy., Hatos A; Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy., Chemes LB; Instituto de Investigaciones Biotecnológicas 'Dr. Rodolfo A. Ugalde'', IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina., Iserte JA; Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina., Méndez NA; Instituto de Investigaciones Biotecnológicas 'Dr. Rodolfo A. Ugalde'', IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina., Garrone NA; Instituto de Investigaciones Biotecnológicas 'Dr. Rodolfo A. Ugalde'', IIB-UNSAM, IIBIO-CONICET, Universidad Nacional de SanMartín, CP1650 San Martín, Buenos Aires, Argentina., Saldaño TE; Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina., Marchetti J; Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina., Rueda AJV; Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina., Bernadó P; Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier 34090, France., Blackledge M; Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France., Cordeiro TN; Centre de Biochimie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier 34090, France.; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras 2780-157, Portugal., Fagerberg E; Theoretical Chemistry, Lund University, Lund, POB 124, SE-221 00, Sweden., Forman-Kay JD; Molecular Medicine Program, Hospital for Sick Children, Toronto, M5G 1X8, Ontario, Canada.; Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Ontario, Canada., Fornasari MS; Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina., Gibson TJ; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany., Gomes GW; Department of Physics, University of Toronto, Toronto, M5S 1A7, Ontario, Canada.; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, L5L 1C6, Ontario, Canada., Gradinaru CC; Department of Physics, University of Toronto, Toronto, M5S 1A7, Ontario, Canada.; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, L5L 1C6, Ontario, Canada., Head-Gordon T; Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering University of California, Berkeley, CA 94720, USA., Jensen MR; Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, F-38000, France., Lemke EA; Biocentre, Johannes Gutenberg-University Mainz, Mainz 55128, Germany.; Institute of Molecular Biology, Mainz 55128, Germany., Longhi S; Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille 13288, France., Marino-Buslje C; Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, C1405BWE, Argentina., Minervini G; Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy., Mittag T; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA., Monzon AM; Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy., Pappu RV; Department of Biomedical Engineering, Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA., Parisi G; Laboratorio de Química y Biología Computacional, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal B1876BXD, Buenos Aires, Argentina., Ricard-Blum S; Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, Villeurbanne, 69629 Lyon Cedex 07, France., Ruff KM; Department of Biomedical Engineering, Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, MO 63130, USA., Salladini E; Aix-Marseille University, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille 13288, France., Skepö M; Theoretical Chemistry, Lund University, Lund, POB 124, SE-221 00, Sweden.; LINXS - Lund Institute of Advanced Neutron and X-ray Science, Lund 223 70, Sweden., Svergun D; European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22607, Germany., Vallet SD; Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, Villeurbanne, 69629 Lyon Cedex 07, France., Varadi M; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK., Tompa P; VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology, Brussels 1050, Belgium.; Structural Biology Brussels, Bioengineering Sciences Department, Vrije Universiteit Brussel, Brussels 1050, Belgium.; Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary., Tosatto SCE; Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy., Piovesan D; Dept. of Biomedical Sciences, University of Padua, Padova 35131, Italy.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2021 Jan 08; Vol. 49 (D1), pp. D404-D411.

Correction to "A 3D Model of Human Lysyl Oxidase, A Cross-Linking Enzyme".

Autor: Vallet SD, Guéroult M, Belloy N, Dauchez M, Ricard-Blum S

Publikováno v: ACS omega [ACS Omega] 2020 Jun 02; Vol. 5 (23), pp. 14202. Date of Electronic Publication: 2020 Jun 02 (Print Publication: 2020).