A Perspective on the Prospective Use of AI in Protein Structure Prediction.

Autor: Versini R; Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France., Sritharan S; Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France., Aykac Fas B; Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France., Tubiana T; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France., Aimeur SZ; Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France., Henri J; Sorbonne Université, CNRS, Laboratoire de Biologie, Computationnelle et Quantitative UMR 7238, Institut de Biologie Paris-Seine, 4 Place Jussieu, F-75005 Paris, France., Erard M; Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France., Nüsse O; Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France., Andreani J; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France., Baaden M; Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France., Fuchs P; Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France.; Université de Paris, UFR Sciences du Vivant, 75013 Paris, France., Galochkina T; Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France., Chatzigoulas A; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.; Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece., Cournia Z; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.; Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, 15784 Athens, Greece., Santuz H; Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France., Sacquin-Mora S; Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France., Taly A; Laboratoire de Biochimie Théorique, CNRS (UPR9080), Université Paris Cité, F-75005 Paris, France.

Publikováno v: Journal of chemical information and modeling [J Chem Inf Model] 2024 Jan 08; Vol. 64 (1), pp. 26-41. Date of Electronic Publication: 2023 Dec 20.

Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs.

Autor: Lambrughi M; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.; Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milano, Italy., Maiani E; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark., Aykac Fas B; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark., Shaw GS; Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada., Kragelund BB; Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark., Lindorff-Larsen K; Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark., Teilum K; Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark., Invernizzi G; Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark., Papaleo E; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark.

Publikováno v: Frontiers in molecular biosciences [Front Mol Biosci] 2021 Jun 28; Vol. 8, pp. 676235. Date of Electronic Publication: 2021 Jun 28 (Print Publication: 2021).

Predicting Mutation-Induced Allosteric Changes in Structures and Conformational Ensembles of the ABL Kinase Using AlphaFold2 Adaptations with Alanine Sequence Scanning.

Autor: Raisinghani, Nishank¹ (AUTHOR) nishankr@stanford.edu, Alshahrani, Mohammed¹ (AUTHOR) alshahrani@chapman.edu, Gupta, Grace¹ (AUTHOR) grgupta@chapman.edu, Verkhivker, Gennady^1,2 (AUTHOR) verkhivk@chapman.edu

Publikováno v: International Journal of Molecular Sciences. Sep2024, Vol. 25 Issue 18, p10082. 24p.

DisProt: intrinsic protein disorder annotation in 2020.

Autor: Hatos A; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy., Hajdu-Soltész B; MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary., Monzon AM; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy., Palopoli N; Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina., Álvarez L; Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina., Aykac-Fas B; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark., Bassot C; Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden., Benítez GI; Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina., Bevilacqua M; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy., Chasapi A; Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica GR-57500, Greece., Chemes L; Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina.; Departamento de Fisiología y Biología Molecular y Celular (DFBMC), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina., Davey NE; Division of Cancer Biology, The Institute of Cancer Research, Chelsea, London SW3 6BJ, UK., Davidović R; Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade 11001, Serbia., Dunker AK; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, IN 46202, USA., Elofsson A; Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden., Gobeill J; Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland., Foutel NSG; Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina., Sudha G; Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden., Guharoy M; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.; VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium., Horvath T; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary., Iglesias V; Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain., Kajava AV; 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., Kovacs OP; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary., Lamb J; Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden., Lambrughi M; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark., Lazar T; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.; VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium., Leclercq JY; Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, Montpellier 34293, France., Leonardi E; Department of Woman and Child Health, University of Padova, Padova 35127, Italy.; Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova 35127, Italy., Macedo-Ribeiro S; Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal., Macossay-Castillo M; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.; VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium., Maiani E; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark., Manso JA; Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal., Marino-Buslje C; Bioinformatics Unit. Fundación Instituto Leloir, Ciudad de Buenos Aires C1405BWE, Argentina., Martínez-Pérez E; Bioinformatics Unit. Fundación Instituto Leloir, Ciudad de Buenos Aires C1405BWE, Argentina., Mészáros B; MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary., Mičetić I; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy., Minervini G; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy., Murvai N; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary., Necci M; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy., Ouzounis CA; Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica GR-57500, Greece., Pajkos M; MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary., Paladin L; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy., Pancsa R; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary., Papaleo E; Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark.; Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen DK-2200, Denmark., Parisi G; Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Bernal, Buenos Aires B1876BXD, Argentina., Pasche E; Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland., Barbosa Pereira PJ; Instituto de Biologia Molecular e Celular (IBMC) and Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal., Promponas VJ; Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY 1678, Cyprus., Pujols J; Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain., Quaglia F; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy., Ruch P; Swiss Institute of Bioinformatics and HES-SO \ HEG, Geneva 1200, Switzerland., Salvatore M; Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Box 1031, Solna 17121, Sweden., Schad E; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary., Szabo B; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary., Szaniszló T; MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary., Tamana S; Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, CY 1678, Cyprus., Tantos A; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary., Veljkovic N; Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade 11001, Serbia., Ventura S; Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain., Vranken W; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium.; VIB-VUB Center for Structural Biology, Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.; Interuniversity Institute of Bioinformatics in Brussels (IB2), ULB-VUB, Brussels 1050, Belgium., Dosztányi Z; MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary., Tompa P; 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., Tosatto SCE; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.; CNR Institute of Neurosceince, Padova 35121, Italy., Piovesan D; Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2020 Jan 08; Vol. 48 (D1), pp. D269-D276.

Assessment of Disordered Linker Predictions in the CAID2 Experiment.

Autor: Wang, Kui¹ (AUTHOR) wangkui@nankai.edu.cn, Hu, Gang¹ (AUTHOR) huggs@nankai.edu.cn, Wu, Zhonghua² (AUTHOR) wuzhh@nankai.edu.cn, Uversky, Vladimir N.³ (AUTHOR) vuversky@usf.edu, Kurgan, Lukasz⁴ (AUTHOR) lkurgan@vcu.edu

Publikováno v: Biomolecules (2218-273X). Mar2024, Vol. 14 Issue 3, p287. 14p.