TY - CHAP AU - Erdős, Gábor AU - Dosztányi, Zsuzsanna ED - Munishwar, Nath Gupta ED - Vladimir, N. Uversky TI - Prediction of protein structure and intrinsic disorder in the era of deep learning T2 - Structure and Intrinsic Disorder in Enzymology PB - Elsevier CY - London CY - San Diego (CA) SN - 9780323995337 PY - 2023 SP - 199 EP - 224 PG - 26 DO - 10.1016/B978-0-323-99533-7.00007-8 UR - https://m2.mtmt.hu/api/publication/33286659 ID - 33286659 LA - English DB - MTMT ER - TY - JOUR AU - Necci, M. AU - Piovesan, D. AU - Hoque, M.T. AU - Walsh, I. AU - Iqbal, S. AU - Vendruscolo, M. AU - Sormanni, P. AU - Wang, C. AU - Raimondi, D. AU - Sharma, R. AU - Zhou, Y. AU - Litfin, T. AU - Galzitskaya, O.V. AU - Lobanov, M.Y. AU - Vranken, W. AU - Wallner, B. AU - Mirabello, C. AU - Malhis, N. AU - Dosztányi, Zsuzsanna AU - Erdős, Gábor AU - Mészáros, B. AU - Gao, J. AU - Wang, K. AU - Hu, G. AU - Wu, Z. AU - Sharma, A. AU - Hanson, J. AU - Paliwal, K. AU - Callebaut, I. AU - Bitard-Feildel, T. AU - Orlando, G. AU - Peng, Z. AU - Xu, J. AU - Wang, S. AU - Jones, D.T. AU - Cozzetto, D. AU - Meng, F. AU - Yan, J. AU - Gsponer, J. AU - Cheng, J. AU - Wu, T. AU - Kurgan, L. AU - Promponas, V.J. AU - Tamana, S. AU - Marino-Buslje, C. AU - Martínez-Pérez, E. AU - Chasapi, A. AU - Ouzounis, C. AU - Dunker, A.K. AU - Kajava, A.V. AU - Leclercq, J.Y. AU - Aykac-Fas, B. AU - Lambrughi, M. AU - Maiani, E. AU - Papaleo, E. AU - Chemes, L.B. AU - Álvarez, L. AU - González-Foutel, N.S. AU - Iglesias, V. AU - Pujols, J. AU - Ventura, S. AU - Palopoli, N. AU - Benítez, G.I. AU - Parisi, G. AU - Bassot, C. AU - Elofsson, A. AU - Govindarajan, S. AU - Lamb, J. AU - Salvatore, M. AU - Hatos, András AU - Monzon, A.M. AU - Bevilacqua, M. AU - Mičetić, I. AU - Minervini, G. AU - Paladin, L. AU - Quaglia, F. AU - Leonardi, E. AU - Davey, N. AU - Horváth, Tamás AU - Kovacs, O.P. AU - Murvai, Nikoletta AU - Pancsa, Rita AU - Schád, Éva AU - Szabó, Beáta AU - Tantos, Ágnes AU - Macedo-Ribeiro, S. AU - Manso, J.A. AU - Pereira, P.J.B. AU - Davidović, R. AU - Veljkovic, N. AU - Hajdu-Soltész, B. AU - Pajkos, M. AU - Szaniszló, Tamás AU - Guharoy, M. AU - Lazar, T. AU - Macossay-Castillo, M. AU - Tompa, Péter AU - Tosatto, S.C.E. TI - Critical assessment of protein intrinsic disorder prediction JF - NATURE METHODS J2 - NAT METHODS VL - 18 PY - 2021 IS - 5 SP - 472 EP - 481 PG - 10 SN - 1548-7091 DO - 10.1038/s41592-021-01117-3 UR - https://m2.mtmt.hu/api/publication/32009587 ID - 32009587 N1 - Department of Biomedical Sciences, University of Padua, Padua, Italy Computer Science, University of New Orleans, New Orleans, LA, United States Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore Center for the Development of Therapeutics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom Department of Medicine, Columbia University, New York, NY, United States ESAT-STADIUS, KU Leuven, Leuven, Belgium Fiji National University, Suva, Fiji Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, Australia Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russian Federation Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel, Brussels, Belgium Division of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada MTA-ELTE Lendulet Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China RIKEN Center for Integrative Medical Sciences, Yokohama, Japan Griffith University, Brisbane, QLD, Australia School of Engineering and Physics, University of the South Pacific, Suva, Fiji Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD, Australia Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France Switch Laboratorium, VIB-KU Leuven, Leuven, Belgium Center for Applied Mathematics, Tianjin University, Tianjin, China Toyota Technological Institute at Chicago, Chicago, IL, United States University College London, London, United Kingdom Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, SC, United States Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus Bioinformatics Unit, Fundación Instituto Leloir, Avda, Patricias Argentinas, Buenos Aires, Argentina Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States Centre de Recherche en Biologie cellulaire de Montpellier, University of Montpellier, Montpellier, France Danish Cancer Society Research Center, Copenhagen, Denmark Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes – CONICET, Bernal, Buenos Aires, Argentina Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden Department of Biology, Section of Computational and RNA Biology, Copenhagen University, Copenhagen, Denmark Department of Woman and Child Health, Univerisity of Padova – Pediatric Research Institute, Città della Speranza, Padova, Italy Division of Cancer Biology, The Institute of Cancer Research, Chelsea, London, United Kingdom Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal Vinča Institute of Nuclear Sciences – National Institute of thе Republic of Serbia, University of Belgrade, Belgrade, Serbia MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary VIB-VUB Center for Structural Biology, Brussels, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium Export Date: 11 May 2021 Correspondence Address: Tosatto, S.C.E.; Department of Biomedical Sciences, Italy; email: silvio.tosatto@unipd.it Funding details: Natural Science Foundation of Tianjin City, 18JCYBJC24900 Funding details: Tianjin Science and Technology Committee, 13ZCZDGX01099 Funding details: National Science Foundation, NSF, 1617369 Funding details: Agence Nationale de la Recherche, ANR, ANR-14-CE10–0021, ANR-17-CE12–0016 Funding details: Australian Research Council, ARC, DP180102060 Funding details: Ministero dell’Istruzione, dell’Università e della Ricerca, MIUR, 2017483NH8 Funding details: Japan Agency for Medical Research and Development, AMED, 16cm0106320h0001 Funding details: Eötvös Loránd Tudományegyetem, ELTE, ED-18-1-2019-0030 Funding details: Fonds Wetenschappelijk Onderzoek, FWO Funding details: Hungarian Scientific Research Fund, OTKA, K124670, K131702 Funding details: Magyar Tudományos Akadémia, MTA, LP2014‐18 Funding details: Natural Sciences and Engineering Research Council of Canada, NSERC, 298328 Funding details: National Natural Science Foundation of China, NSFC, 11701296, 31970649 Funding details: Horizon 2020 Framework Programme, H2020, 778247 Funding text 1: Development of the predictors was supported in part by the National Science Foundation (grant no. 1617369), Natural Sciences and Engineering Research Council of Canada (grant no. 298328), Tianjin Municipal Science and Technology Commission (grant no. 13ZCZDGX01099), National Natural Science Foundation of China (grant nos. 31970649 and 11701296), Natural Science Foundation of Tianjin (grant no. 18JCYBJC24900), Japan Agency for Medical Research and Development (grant no. 16cm0106320h0001), Australian Research Council (no. DP180102060), Research Foundation Flanders (project no. G.0328.16N) and Agence Nationale de la Recherche (nos. ANR-14-CE10–0021 and ANR-17-CE12–0016). O.V.T. and M.L. carried out this work as part of the state task “Bioinformatics and proteomics studies of proteins and their complexes” (no. 0115-2019-004). Z.D. acknowledges funding from the ELTE Thematic Excellence Programme (no. ED-18-1-2019-0030), supported by the Hungarian Ministry for Innovation and Technology, and the ‘Lendület’ grant from the Hungarian Academy of Sciences (no. LP2014‐18). P.T. acknowledges the Hungarian Scientific Research Fund (grant nos. K124670 and K131702). This project received funding from the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement no. 778247, the Italian Ministry of University and Research (PRIN 2017, grant no. 2017483NH8) and ELIXIR, the European infrastructure for biological data. Department of Biomedical Sciences, University of Padua, Padua, Italy Computer Science, University of New Orleans, New Orleans, LA, United States Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore Center for the Development of Therapeutics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom Department of Medicine, Columbia University, New York, NY, United States ESAT-STADIUS, KU Leuven, Leuven, Belgium Fiji National University, Suva, Fiji Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, Australia Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russian Federation Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel, Brussels, Belgium Division of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada MTA-ELTE Lendulet Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China RIKEN Center for Integrative Medical Sciences, Yokohama, Japan Griffith University, Brisbane, QLD, Australia School of Engineering and Physics, University of the South Pacific, Suva, Fiji Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD, Australia Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France Switch Laboratorium, VIB-KU Leuven, Leuven, Belgium Center for Applied Mathematics, Tianjin University, Tianjin, China Toyota Technological Institute at Chicago, Chicago, IL, United States University College London, London, United Kingdom Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, SC, United States Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus Bioinformatics Unit, Fundación Instituto Leloir, Avda, Patricias Argentinas, Buenos Aires, Argentina Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States Centre de Recherche en Biologie cellulaire de Montpellier, University of Montpellier, Montpellier, France Danish Cancer Society Research Center, Copenhagen, Denmark Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes – CONICET, Bernal, Buenos Aires, Argentina Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden Department of Biology, Section of Computational and RNA Biology, Copenhagen University, Copenhagen, Denmark Department of Woman and Child Health, Univerisity of Padova – Pediatric Research Institute, Città della Speranza, Padova, Italy Division of Cancer Biology, The Institute of Cancer Research, Chelsea, London, United Kingdom Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal Vinča Institute of Nuclear Sciences – National Institute of thе Republic of Serbia, University of Belgrade, Belgrade, Serbia MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary VIB-VUB Center for Structural Biology, Brussels, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium Cited By :6 Export Date: 2 September 2021 Correspondence Address: Tosatto, S.C.E.; Department of Biomedical Sciences, Italy; email: silvio.tosatto@unipd.it Chemicals/CAS: Intrinsically Disordered Proteins Funding details: National Science Foundation, NSF, 1617369, 1759934, 1763246 Funding details: Japan Agency for Medical Research and Development, AMED, 16cm0106320h0001 Funding details: Horizon 2020 Framework Programme, H2020, 778247 Funding details: Natural Sciences and Engineering Research Council of Canada, NSERC, 298328 Funding details: Australian Research Council, ARC, DP180102060 Funding details: Agence Nationale de la Recherche, ANR, ANR-14-CE10–0021, ANR-17-CE12–0016 Funding details: National Natural Science Foundation of China, NSFC, 11701296, 31970649 Funding details: Fonds Wetenschappelijk Onderzoek, FWO Funding details: Ministero dell’Istruzione, dell’Università e della Ricerca, MIUR, 2017483NH8 Funding details: Hungarian Scientific Research Fund, OTKA, K124670, K131702 Funding details: Magyar Tudományos Akadémia, MTA, LP2014‐18 Funding details: Natural Science Foundation of Tianjin City, 18JCYBJC24900 Funding details: Eötvös Loránd Tudományegyetem, ELTE, ED-18-1-2019-0030 Funding details: Tianjin Science and Technology Committee, 13ZCZDGX01099 Funding text 1: Development of the predictors was supported in part by the National Science Foundation (grant no. 1617369), Natural Sciences and Engineering Research Council of Canada (grant no. 298328), Tianjin Municipal Science and Technology Commission (grant no. 13ZCZDGX01099), National Natural Science Foundation of China (grant nos. 31970649 and 11701296), Natural Science Foundation of Tianjin (grant no. 18JCYBJC24900), Japan Agency for Medical Research and Development (grant no. 16cm0106320h0001), Australian Research Council (no. DP180102060), Research Foundation Flanders (project no. G.0328.16N) and Agence Nationale de la Recherche (nos. ANR-14-CE10–0021 and ANR-17-CE12–0016). O.V.T. and M.L. carried out this work as part of the state task “Bioinformatics and proteomics studies of proteins and their complexes” (no. 0115-2019-004). Z.D. acknowledges funding from the ELTE Thematic Excellence Programme (no. ED-18-1-2019-0030), supported by the Hungarian Ministry for Innovation and Technology, and the ‘Lendület’ grant from the Hungarian Academy of Sciences (no. LP2014‐18). P.T. acknowledges the Hungarian Scientific Research Fund (grant nos. K124670 and K131702). This project received funding from the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement no. 778247, the Italian Ministry of University and Research (PRIN 2017, grant no. 2017483NH8) and ELIXIR, the European infrastructure for biological data. Department of Biomedical Sciences, University of Padua, Padua, Italy Computer Science, University of New Orleans, New Orleans, LA, United States Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore Center for the Development of Therapeutics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom Department of Medicine, Columbia University, New York, NY, United States ESAT-STADIUS, KU Leuven, Leuven, Belgium Fiji National University, Suva, Fiji Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, Australia Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russian Federation Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel, Brussels, Belgium Division of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada MTA-ELTE Lendulet Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China RIKEN Center for Integrative Medical Sciences, Yokohama, Japan Griffith University, Brisbane, QLD, Australia School of Engineering and Physics, University of the South Pacific, Suva, Fiji Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD, Australia Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France Switch Laboratorium, VIB-KU Leuven, Leuven, Belgium Center for Applied Mathematics, Tianjin University, Tianjin, China Toyota Technological Institute at Chicago, Chicago, IL, United States University College London, London, United Kingdom Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, SC, United States Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus Bioinformatics Unit, Fundación Instituto Leloir, Avda, Patricias Argentinas, Buenos Aires, Argentina Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States Centre de Recherche en Biologie cellulaire de Montpellier, University of Montpellier, Montpellier, France Danish Cancer Society Research Center, Copenhagen, Denmark Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes – CONICET, Bernal, Buenos Aires, Argentina Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden Department of Biology, Section of Computational and RNA Biology, Copenhagen University, Copenhagen, Denmark Department of Woman and Child Health, Univerisity of Padova – Pediatric Research Institute, Città della Speranza, Padova, Italy Division of Cancer Biology, The Institute of Cancer Research, Chelsea, London, United Kingdom Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal Vinča Institute of Nuclear Sciences – National Institute of thе Republic of Serbia, University of Belgrade, Belgrade, Serbia MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary VIB-VUB Center for Structural Biology, Brussels, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium Cited By :6 Export Date: 3 September 2021 Correspondence Address: Tosatto, S.C.E.; Department of Biomedical Sciences, Italy; email: silvio.tosatto@unipd.it Chemicals/CAS: Intrinsically Disordered Proteins Funding details: National Science Foundation, NSF, 1617369, 1759934, 1763246 Funding details: Japan Agency for Medical Research and Development, AMED, 16cm0106320h0001 Funding details: Horizon 2020 Framework Programme, H2020, 778247 Funding details: Natural Sciences and Engineering Research Council of Canada, NSERC, 298328 Funding details: Australian Research Council, ARC, DP180102060 Funding details: Agence Nationale de la Recherche, ANR, ANR-14-CE10–0021, ANR-17-CE12–0016 Funding details: National Natural Science Foundation of China, NSFC, 11701296, 31970649 Funding details: Fonds Wetenschappelijk Onderzoek, FWO Funding details: Ministero dell’Istruzione, dell’Università e della Ricerca, MIUR, 2017483NH8 Funding details: Hungarian Scientific Research Fund, OTKA, K124670, K131702 Funding details: Magyar Tudományos Akadémia, MTA, LP2014‐18 Funding details: Natural Science Foundation of Tianjin City, 18JCYBJC24900 Funding details: Eötvös Loránd Tudományegyetem, ELTE, ED-18-1-2019-0030 Funding details: Tianjin Science and Technology Committee, 13ZCZDGX01099 Funding text 1: Development of the predictors was supported in part by the National Science Foundation (grant no. 1617369), Natural Sciences and Engineering Research Council of Canada (grant no. 298328), Tianjin Municipal Science and Technology Commission (grant no. 13ZCZDGX01099), National Natural Science Foundation of China (grant nos. 31970649 and 11701296), Natural Science Foundation of Tianjin (grant no. 18JCYBJC24900), Japan Agency for Medical Research and Development (grant no. 16cm0106320h0001), Australian Research Council (no. DP180102060), Research Foundation Flanders (project no. G.0328.16N) and Agence Nationale de la Recherche (nos. ANR-14-CE10–0021 and ANR-17-CE12–0016). O.V.T. and M.L. carried out this work as part of the state task “Bioinformatics and proteomics studies of proteins and their complexes” (no. 0115-2019-004). Z.D. acknowledges funding from the ELTE Thematic Excellence Programme (no. ED-18-1-2019-0030), supported by the Hungarian Ministry for Innovation and Technology, and the ‘Lendület’ grant from the Hungarian Academy of Sciences (no. LP2014‐18). P.T. acknowledges the Hungarian Scientific Research Fund (grant nos. K124670 and K131702). This project received funding from the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement no. 778247, the Italian Ministry of University and Research (PRIN 2017, grant no. 2017483NH8) and ELIXIR, the European infrastructure for biological data. Department of Biomedical Sciences, University of Padua, Padua, Italy Computer Science, University of New Orleans, New Orleans, LA, United States Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore Center for the Development of Therapeutics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom Department of Medicine, Columbia University, New York, NY, United States ESAT-STADIUS, KU Leuven, Leuven, Belgium Fiji National University, Suva, Fiji Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, Australia Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russian Federation Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel, Brussels, Belgium Division of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada MTA-ELTE Lendulet Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China RIKEN Center for Integrative Medical Sciences, Yokohama, Japan Griffith University, Brisbane, QLD, Australia School of Engineering and Physics, University of the South Pacific, Suva, Fiji Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD, Australia Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France Switch Laboratorium, VIB-KU Leuven, Leuven, Belgium Center for Applied Mathematics, Tianjin University, Tianjin, China Toyota Technological Institute at Chicago, Chicago, IL, United States University College London, London, United Kingdom Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, SC, United States Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus Bioinformatics Unit, Fundación Instituto Leloir, Avda, Patricias Argentinas, Buenos Aires, Argentina Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States Centre de Recherche en Biologie cellulaire de Montpellier, University of Montpellier, Montpellier, France Danish Cancer Society Research Center, Copenhagen, Denmark Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina Departament de Bioquimica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes – CONICET, Bernal, Buenos Aires, Argentina Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Solna, Sweden Department of Biology, Section of Computational and RNA Biology, Copenhagen University, Copenhagen, Denmark Department of Woman and Child Health, Univerisity of Padova – Pediatric Research Institute, Città della Speranza, Padova, Italy Division of Cancer Biology, The Institute of Cancer Research, Chelsea, London, United Kingdom Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal Vinča Institute of Nuclear Sciences – National Institute of thе Republic of Serbia, University of Belgrade, Belgrade, Serbia MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary VIB-VUB Center for Structural Biology, Brussels, Belgium Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium Cited By :9 Export Date: 6 September 2021 Correspondence Address: Tosatto, S.C.E.; Department of Biomedical Sciences, Italy; email: silvio.tosatto@unipd.it Chemicals/CAS: Intrinsically Disordered Proteins Funding details: National Science Foundation, NSF, 1617369, 1759934, 1763246 Funding details: Japan Agency for Medical Research and Development, AMED, 16cm0106320h0001 Funding details: Horizon 2020 Framework Programme, H2020, 778247 Funding details: Natural Sciences and Engineering Research Council of Canada, NSERC, 298328 Funding details: Australian Research Council, ARC, DP180102060 Funding details: Agence Nationale de la Recherche, ANR, ANR-14-CE10–0021, ANR-17-CE12–0016 Funding details: National Natural Science Foundation of China, NSFC, 11701296, 31970649 Funding details: Fonds Wetenschappelijk Onderzoek, FWO Funding details: Ministero dell’Istruzione, dell’Università e della Ricerca, MIUR, 2017483NH8 Funding details: Hungarian Scientific Research Fund, OTKA, K124670, K131702 Funding details: Magyar Tudományos Akadémia, MTA, LP2014‐18 Funding details: Natural Science Foundation of Tianjin City, 18JCYBJC24900 Funding details: Eötvös Loránd Tudományegyetem, ELTE, ED-18-1-2019-0030 Funding details: Tianjin Science and Technology Committee, 13ZCZDGX01099 Funding text 1: Development of the predictors was supported in part by the National Science Foundation (grant no. 1617369), Natural Sciences and Engineering Research Council of Canada (grant no. 298328), Tianjin Municipal Science and Technology Commission (grant no. 13ZCZDGX01099), National Natural Science Foundation of China (grant nos. 31970649 and 11701296), Natural Science Foundation of Tianjin (grant no. 18JCYBJC24900), Japan Agency for Medical Research and Development (grant no. 16cm0106320h0001), Australian Research Council (no. DP180102060), Research Foundation Flanders (project no. G.0328.16N) and Agence Nationale de la Recherche (nos. ANR-14-CE10–0021 and ANR-17-CE12–0016). O.V.T. and M.L. carried out this work as part of the state task “Bioinformatics and proteomics studies of proteins and their complexes” (no. 0115-2019-004). Z.D. acknowledges funding from the ELTE Thematic Excellence Programme (no. ED-18-1-2019-0030), supported by the Hungarian Ministry for Innovation and Technology, and the ‘Lendület’ grant from the Hungarian Academy of Sciences (no. LP2014‐18). P.T. acknowledges the Hungarian Scientific Research Fund (grant nos. K124670 and K131702). This project received funding from the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement no. 778247, the Italian Ministry of University and Research (PRIN 2017, grant no. 2017483NH8) and ELIXIR, the European infrastructure for biological data. Department of Biomedical Sciences, University of Padua, Padua, Italy Computer Science, University of New Orleans, New Orleans, LA, United States Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Singapore Center for the Development of Therapeutics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom Department of Medicine, Columbia University, New York, NY, United States ESAT-STADIUS, KU Leuven, Leuven, Belgium Fiji National University, Suva, Fiji Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, Australia Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russian Federation Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russian Federation Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel, Brussels, Belgium Division of Bioinformatics, Department of Physics, Chemistry, and Biology, Linköping University, Linköping, Sweden Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada MTA-ELTE Lendulet Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany School of Mathematical Sciences and LPMC, Nankai University, Tianjin, China School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China RIKEN Center for Integrative Medical Sciences, Yokohama, Japan Griffith University, Brisbane, QLD, Australia School of Engineering and Physics, University of the South Pacific, Suva, Fiji Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD, Australia Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, Paris, France Switch Laboratorium, VIB-KU Leuven, Leuven, Belgium Center for Applied Mathematics, Tianjin University, Tianjin, China Toyota Technological Institute at Chicago, Chicago, IL, United States University College London, London, United Kingdom Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, SC, United States Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus Bioinformatics Unit, Fundación Instituto Leloir, Avda, Patricias Argentinas, Buenos Aires, Argentina Chemical Process & E AB - Intrinsically disordered proteins, defying the traditional protein structure–function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in prediction of intrinsically disordered regions and the subset of residues involved in binding. A total of 43 methods were evaluated on a dataset of 646 proteins from DisProt. The best methods use deep learning techniques and notably outperform physicochemical methods. The top disorder predictor has Fmax = 0.483 on the full dataset and Fmax = 0.792 following filtering out of bona fide structured regions. Disordered binding regions remain hard to predict, with Fmax = 0.231. Interestingly, computing times among methods can vary by up to four orders of magnitude. © 2021, The Author(s), under exclusive licence to Springer Nature America, Inc. LA - English DB - MTMT ER - TY - JOUR AU - Necci, Marco AU - Piovesan, Damiano AU - Clementel, Damiano AU - Dosztányi, Zsuzsanna AU - Tosatto, Silvio C E TI - MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins JF - BIOINFORMATICS J2 - BIOINFORMATICS VL - 36 PY - 2020 IS - 22-23 SP - 5533 EP - 5534 PG - 2 SN - 1367-4803 DO - 10.1093/bioinformatics/btaa1045 UR - https://m2.mtmt.hu/api/publication/31992673 ID - 31992673 N1 - Department of Biomedical Sciences, University of Padua, Padova, 35121, Italy MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary Cited By :12 Export Date: 30 March 2022 CODEN: BOINF Correspondence Address: Tosatto, S.C.E.; Department of Biomedical Sciences, Italy; email: silvio.tosatto@unipd.it LA - English DB - MTMT ER - TY - JOUR AU - Gáspárné Csizmadia, Georgina AU - Erdős, Gábor AU - Tordai, Hedvig AU - Padányi, Rita AU - Tosatto, Silvio AU - Dosztányi, Zsuzsanna AU - Hegedűs, Tamás TI - The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 49 PY - 2020 IS - D1 SP - D355 EP - D360 SN - 0305-1048 DO - 10.1093/nar/gkaa954 UR - https://m2.mtmt.hu/api/publication/31641470 ID - 31641470 N1 - Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, 1117, Hungary Department of Biomedical Sciences, University of Padua, Padua, 35131, Italy Cited By :3 Export Date: 31 March 2022 CODEN: NARHA Correspondence Address: Hegedűs, T.; Department of Biophysics and Radiation Biology, Hungary; email: hegedus@hegelab.org LA - English DB - MTMT ER - TY - JOUR AU - Kastano, Kristina AU - Erdős, Gábor AU - Mier, Pablo AU - Alanis-Lobato, Gregorio AU - Promponas, Vasilis J. AU - Dosztányi, Zsuzsanna AU - Andrade-Navarro, Miguel A. TI - Evolutionary Study of Disorder in Protein Sequences JF - BIOMOLECULES J2 - BIOMOLECULES VL - 10 PY - 2020 IS - 10 SN - 2218-273X DO - 10.3390/biom10101413 UR - https://m2.mtmt.hu/api/publication/31634342 ID - 31634342 N1 - Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Mainz, 55128, Germany Bioinformatics Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, MTA-ELTE Momentum, Budapest, H-1117, Hungary Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, 2109, Cyprus Cited By :7 Export Date: 30 March 2022 Correspondence Address: Andrade-Navarro, M.A.; Faculty of Biology, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, Germany; email: andrade@uni-mainz.de LA - English DB - MTMT ER - TY - JOUR AU - Erdős, Gábor AU - Dosztányi, Zsuzsanna TI - Analyzing Protein Disorder with IUPred2A JF - CURRENT PROTOCOLS IN BIOINFORMATICS J2 - CURR PROTOC BIOINFORMATICS VL - 70 PY - 2020 IS - 1 SN - 1934-3396 DO - 10.1002/cpbi.99 UR - https://m2.mtmt.hu/api/publication/31277690 ID - 31277690 N1 - Cited By :62 Export Date: 31 March 2022 Correspondence Address: Dosztányi, Z.; Department of Biochemistry, Hungary; email: dosztanyi@caesar.elte.hu LA - English DB - MTMT ER - TY - JOUR AU - Mészáros, Bálint AU - Erdős, Gábor AU - Szabó, Beáta AU - Schád, Éva AU - Tantos, Ágnes AU - Horváth, Tamás AU - Horváth, Tamás AU - Murvai, Nikoletta AU - Kovács, Orsolya P AU - Kovács, Márton AU - Tosatto, Silvio C E AU - Tompa, Péter AU - Dosztányi, Zsuzsanna AU - Pancsa, Rita TI - PhaSePro. the database of proteins driving liquid-liquid phase separation. TS - the database of proteins driving liquid-liquid phase separation. JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 48 PY - 2020 IS - D1 SP - D360 EP - D367 SN - 0305-1048 DO - 10.1093/nar/gkz848 UR - https://m2.mtmt.hu/api/publication/30922925 ID - 30922925 N1 - Funding Agency and Grant Number: Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133, K-124670, K-125340]; Hungarian Academy of SciencesHungarian Academy of Sciences [LP2014-18, PREMIUM-2017-48]; VUB [SRP51, 2019-24]; New National Excellence Programme (UNKP) [ELTE/12653/314(2018)]; National Research Council of Science and Technology (NST) of Korea [NTM2231611]; European Union's Horizon 2020 research and innovation programme [778247] Funding text: Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133 to R.P., K-124670 to P.T. and K-125340 to A.T.]; Hungarian Academy of Sciences [LP2014-18 to Z.D., PREMIUM-2017-48 to R.P.]; VUB [SRP51, 2019-24 to P.T.]; New National Excellence Programme (UNKP) [ELTE/12653/314(2018) to M.K.]; National Research Council of Science and Technology (NST) of Korea [NTM2231611 to P.T.]; European Union's Horizon 2020 research and innovation programme [778247 (IDPfun) to S.T., P.T. and Z.D.]. Funding for open access charge: Hungarian Academy of Sciences. MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, H-1117, Hungary Department of Biomedical Sciences, University of Padova, CNR Institute of Neuroscience, Padova, Italy Structural Biology (CSB), Brussels, Belgium Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium Cited By :9 Export Date: 26 May 2020 CODEN: NARHA Correspondence Address: Pancsa, R.; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesHungary; email: pancsa.rita@ttk.mta.hu Funding details: National Research Council of Science and Technology, NST Funding details: Horizon 2020 Framework Programme, H2020, 778247 Funding details: ELTE/12653/314(2018 Funding details: Magyar Tudományos Akadémia, MTA, PREMIUM-2017-48, LP2014-18, SRP51 Funding details: National Research Council of Science and Technology, NST, NTM2231611 Funding details: Nemzeti Kutatási Fejlesztési és Innovációs Hivatal, NKFI, K-124670, K-125340, FK-128133 Funding text 1: Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133 to R.P., K-124670 to P.T. and K-125340 to A.T.]; Hungarian Academy of Sciences [LP2014-18 to Z.D., PREMIUM-2017-48 to R.P.]; VUB [SRP51, 2019–24 to P.T.]; New National Excellence Programme (UNKP) [ELTE/12653/314(2018) to M.K.]; National Research Council of Science and Technology (NST) of Korea [NTM2231611 to P.T.]; European Union’s Horizon 2020 research and innovation programme [778247 (IDPfun) to S.T., P.T. and Z.D.]. Funding for open access charge: Hungarian Academy of Sciences. Conflict of interest statement. None declared. MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, H-1117, Hungary Department of Biomedical Sciences, University of Padova, CNR Institute of Neuroscience, Padova, Italy Structural Biology (CSB), Brussels, Belgium Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium Cited By :9 Export Date: 27 May 2020 CODEN: NARHA Correspondence Address: Pancsa, R.; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesHungary; email: pancsa.rita@ttk.mta.hu Funding details: National Research Council of Science and Technology, NST Funding details: Horizon 2020 Framework Programme, H2020, 778247 Funding details: ELTE/12653/314(2018 Funding details: Magyar Tudományos Akadémia, MTA, PREMIUM-2017-48, LP2014-18, SRP51 Funding details: National Research Council of Science and Technology, NST, NTM2231611 Funding details: Nemzeti Kutatási Fejlesztési és Innovációs Hivatal, NKFI, K-124670, K-125340, FK-128133 Funding text 1: Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133 to R.P., K-124670 to P.T. and K-125340 to A.T.]; Hungarian Academy of Sciences [LP2014-18 to Z.D., PREMIUM-2017-48 to R.P.]; VUB [SRP51, 2019–24 to P.T.]; New National Excellence Programme (UNKP) [ELTE/12653/314(2018) to M.K.]; National Research Council of Science and Technology (NST) of Korea [NTM2231611 to P.T.]; European Union’s Horizon 2020 research and innovation programme [778247 (IDPfun) to S.T., P.T. and Z.D.]. Funding for open access charge: Hungarian Academy of Sciences. Conflict of interest statement. None declared. MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, H-1117, Hungary Department of Biomedical Sciences, University of Padova, CNR Institute of Neuroscience, Padova, Italy Structural Biology (CSB), Brussels, Belgium Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium Cited By :9 Export Date: 2 June 2020 CODEN: NARHA Correspondence Address: Pancsa, R.; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesHungary; email: pancsa.rita@ttk.mta.hu Funding details: National Research Council of Science and Technology, NST Funding details: Horizon 2020 Framework Programme, H2020, 778247 Funding details: ELTE/12653/314(2018 Funding details: Magyar Tudományos Akadémia, MTA, PREMIUM-2017-48, LP2014-18, SRP51 Funding details: National Research Council of Science and Technology, NST, NTM2231611 Funding details: Nemzeti Kutatási Fejlesztési és Innovációs Hivatal, NKFI, K-124670, K-125340, FK-128133 Funding text 1: Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133 to R.P., K-124670 to P.T. and K-125340 to A.T.]; Hungarian Academy of Sciences [LP2014-18 to Z.D., PREMIUM-2017-48 to R.P.]; VUB [SRP51, 2019–24 to P.T.]; New National Excellence Programme (UNKP) [ELTE/12653/314(2018) to M.K.]; National Research Council of Science and Technology (NST) of Korea [NTM2231611 to P.T.]; European Union’s Horizon 2020 research and innovation programme [778247 (IDPfun) to S.T., P.T. and Z.D.]. Funding for open access charge: Hungarian Academy of Sciences. Conflict of interest statement. None declared. MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, H-1117, Hungary Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, H-1117, Hungary Department of Biomedical Sciences, University of Padova, CNR Institute of Neuroscience, Padova, Italy Structural Biology (CSB), Brussels, Belgium Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium Cited By :10 Export Date: 12 August 2020 CODEN: NARHA Correspondence Address: Pancsa, R.; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of SciencesHungary; email: pancsa.rita@ttk.mta.hu Chemicals/CAS: protein, 67254-75-5; Proteins Funding details: National Research Council of Science and Technology, NST Funding details: Horizon 2020 Framework Programme, H2020, 778247 Funding details: ELTE/12653/314(2018 Funding details: Magyar Tudományos Akadémia, MTA, PREMIUM-2017-48, LP2014-18, SRP51 Funding details: National Research Council of Science and Technology, NST, NTM2231611 Funding details: Nemzeti Kutatási Fejlesztési és Innovációs Hivatal, NKFI, K-124670, K-125340, FK-128133 Funding text 1: Hungarian National Research, Development, and Innovation Office (NKFIH) [FK-128133 to R.P., K-124670 to P.T. and K-125340 to A.T.]; Hungarian Academy of Sciences [LP2014-18 to Z.D., PREMIUM-2017-48 to R.P.]; VUB [SRP51, 2019–24 to P.T.]; New National Excellence Programme (UNKP) [ELTE/12653/314(2018) to M.K.]; National Research Council of Science and Technology (NST) of Korea [NTM2231611 to P.T.]; European Union’s Horizon 2020 research and innovation programme [778247 (IDPfun) to S.T., P.T. and Z.D.]. Funding for open access charge: Hungarian Academy of Sciences. Conflict of interest statement. None declared. AB - Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid-liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life. While numerous experimental studies report novel cases, the computational identification of LLPS drivers is lagging behind, and many open questions remain about the sequence determinants, composition, regulation and biological relevance of the resulting condensates. Our limited ability to overcome these issues is largely due to the lack of a dedicated LLPS database. Therefore, here we introduce PhaSePro (https://phasepro.elte.hu), an openly accessible, comprehensive, manually curated database of experimentally validated LLPS driver proteins/protein regions. It not only provides a wealth of information on such systems, but improves the standardization of data by introducing novel LLPS-specific controlled vocabularies. PhaSePro can be accessed through an appealing, user-friendly interface and thus has definite potential to become the central resource in this dynamically developing field. LA - English DB - MTMT ER - TY - JOUR AU - Hatos, András AU - Hajdu-Soltész, Borbála AU - Monzon, Alexander M AU - Palopoli, Nicolas AU - Álvarez, Lucía AU - Aykac-Fas, Burcu AU - Bassot, Claudio AU - Benítez, Guillermo I AU - Bevilacqua, Martina AU - Chasapi, Anastasia AU - Chemes, Lucia AU - Davey, Norman E AU - Davidović, Radoslav AU - Dunker, A Keith AU - Elofsson, Arne AU - Gobeill, Julien AU - Foutel, Nicolás S González AU - Sudha, Govindarajan AU - Guharoy, Mainak AU - Horváth, Tamás AU - Iglesias, Valentin AU - Kajava, Andrey V AU - Kovacs, Orsolya P AU - Lamb, John AU - Lambrughi, Matteo AU - Lazar, Tamas AU - Leclercq, Jeremy Y AU - Leonardi, Emanuela AU - Macedo-Ribeiro, Sandra AU - Macossay-Castillo, Mauricio AU - Maiani, Emiliano AU - Manso, José A AU - Marino-Buslje, Cristina AU - Martínez-Pérez, Elizabeth AU - Mészáros, Bálint AU - Mičetić, Ivan AU - Minervini, Giovanni AU - Murvai, Nikoletta AU - Necci, Marco AU - Ouzounis, Christos A AU - Pajkos, Mátyás AU - Paladin, Lisanna AU - Pancsa, Rita AU - Papaleo, Elena AU - Parisi, Gustavo AU - Pasche, Emilie AU - Barbosa Pereira, Pedro J AU - Promponas, Vasilis J AU - Pujols, Jordi AU - Quaglia, Federica AU - Ruch, Patrick AU - Salvatore, Marco AU - Schád, Éva AU - Szabó, Beáta AU - Szaniszló, Tamás AU - Tamana, Stella AU - Tantos, Ágnes AU - Veljkovic, Nevena AU - Ventura, Salvador AU - Vranken, Wim AU - Dosztányi, Zsuzsanna AU - Tompa, Péter AU - Tosatto, Silvio C E AU - Piovesan, Damiano TI - DisProt: intrinsic protein disorder annotation in 2020 JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 48 PY - 2020 IS - D1 SP - D269 EP - D276 SN - 0305-1048 DO - 10.1093/nar/gkz975 UR - https://m2.mtmt.hu/api/publication/30922910 ID - 30922910 N1 - Department of Biomedical Sciences, University of Padova, Padova, 35121, Italy MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, 1117, Hungary Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Bernal, Buenos Aires, B1876BXD, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, DK-2100, Denmark Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden Biological Computation and Process Laboratory, Chemical Process and Energy Resources Institute, Centre for Research and Technology Hellas, Thessalonica, GR-57500, Greece Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina Division of Cancer Biology, Institute of Cancer Research, Chelsea, London, SW3 6BJ, United Kingdom Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade, 11001, Serbia Center for Computational Biology and Bioinformatics, Indiana University School of MedicineIN 46202, United States Swiss Institute of Bioinformatics and HES-SO\HEG, Geneva, 1200, Switzerland Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels, 1050, Belgium Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, H-1117, Hungary Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier, 34293, France Institut de Biologie Computationnelle(IBC), Montpellier, 34095, France Department of Woman and Child Health, University of Padova, Padova, 35127, Italy Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, 35127, Italy Instituto de Biologia Molecular e Celular (IBMC), Instituto de Investigação e Inovação em Saúde (i3S), Universidade Do Porto, Porto, 4200-135, Portugal Bioinformatics Unit. Fundación Instituto Leloir, Ciudad de Buenos Aires, C1405BWE, Argentina Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center, Protein Research University of Copenhagen, Copenhagen, DK-2200, Denmark Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia CY, 1678, Cyprus Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels, 1050, Belgium CNR Institute of Neurosceince, Padova, 35121, Italy Cited By :123 Export Date: 23 September 2022 CODEN: NARHA Correspondence Address: Tosatto, S.C.E.; Department of Biomedical Sciences, Italy; email: silvio.tosatto@unipd.it AB - The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the 'dark' proteome. LA - English DB - MTMT ER - TY - JOUR AU - Pablo, Mier AU - Lisanna, Paladin AU - Stella, Tamana AU - Sophia, Petrosian AU - Hajdu-Soltész, Borbála AU - Annika, Urbanek AU - Aleksandra, Gruca AU - Dariusz, Plewczynski AU - Marcin, Grynberg AU - Pau, Bernadó AU - Gáspári, Zoltán AU - Christos, A. Ouzounis AU - Vasilis, J. Promponas AU - Andrey, V. Kajava AU - John, M. Hancock AU - Silvio, C. E. Tosatto AU - Dosztányi, Zsuzsanna AU - Miguel, A. Andrade-Navarro TI - Disentangling the complexity of low complexity proteins JF - BRIEFINGS IN BIOINFORMATICS J2 - BRIEF BIOINFORM VL - 21 PY - 2020 IS - 2 SP - 458 EP - 472 PG - 15 SN - 1467-5463 DO - 10.1093/bib/bbz007 UR - https://m2.mtmt.hu/api/publication/30418509 ID - 30418509 N1 - Published: 30 January 2019 LA - English DB - MTMT ER - TY - JOUR AU - Mészáros, Bálint AU - Dobson, László AU - Fichó, Erzsébet AU - Simon, István TI - Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 20 PY - 2019 IS - 21 PG - 21 SN - 1661-6596 DO - 10.3390/ijms20215460 UR - https://m2.mtmt.hu/api/publication/30875480 ID - 30875480 N1 - MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter stny 1/c, Budapest, H-1117, Hungary European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, 69117, Germany Protein Structure Research Group, Institute of Enzymology, RCNS, HAS, Magyar Tudósok krt 2, Budapest, H-1117, Hungary Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Magyar Tudósok krt 2, Budapest, H-1117, Hungary Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, Budapest, H-1083, Hungary Cited By :2 Export Date: 31 March 2022 Correspondence Address: Mészáros, B.; MTA-ELTE Momentum Bioinformatics Research Group, Pázmány Péter stny 1/c, Hungary; email: bmeszaros@caesar.elte.hu LA - English DB - MTMT ER -