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20 p, 3.7 MB |
A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation
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Pintado-Grima, Carlos (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Bárcenas, Oriol (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Bartolomé-Nafría, Andrea (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Fornt Suñé, Marc (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Garcia-Pardo, Javier (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Universitat Autònoma de Barcelona
The presence of insoluble protein deposits in tissues and organs is a hallmark of many human pathologies. In addition, the formation of protein aggregates is considered one of the main bottlenecks to producing protein-based therapeutics. [...]
2023 -  10.3390/biophysica3010001
Biophysica, Vol. 3 Núm. 1 (January 2023)
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10 p, 1.9 MB |
A3DyDB : exploring structural aggregation propensities in the yeast proteome
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Garcia-Pardo, Javier (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Badaczewska-Dawid, Aleksandra E. (Iowa State University) ;
Pintado-Grima, Carlos (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Kuriata, Aleksander (University of Warsaw) ;
Kmiecik, Sebastian (University of Warsaw) ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Background: The budding yeast Saccharomyces cerevisiae (S. cerevisiae) is a well-established model system for studying protein aggregation due to the conservation of essential cellular structures and pathways found across eukaryotes. [...]
2023 - 10.1186/s12934-023-02182-3
Microbial cell factories, Vol. 22, Issue 1 (September 2023) , art. 186
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23 p, 5.3 MB |
Selection of an Aptamer against the Enzyme 1-deoxy-D-xylulose-5-phosphate Reductoisomerase from Plasmodium falciparum
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Roca, Carlota (Universitat de Barcelona) ;
Avalos-Padilla, Yunuen (Universitat de Barcelona) ;
Prieto-Simón, Beatriz (Institució Catalana de Recerca i Estudis Avançats) ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ramírez, Miriam (Hospital Clínic i Provincial de Barcelona) ;
Imperial, Santiago (Universitat de Barcelona) ;
Fernàndez-Busquets, Xavier (Universitat de Barcelona) ;
Universitat Autònoma de Barcelona.
Departament de Bioquímica i de Biologia Molecular
The methyl erythritol phosphate (MEP) pathway of isoprenoid biosynthesis is essential for malaria parasites and also for several human pathogenic bacteria, thus representing an interesting target for future antimalarials and antibiotics and for diagnostic strategies. [...]
2022 - 10.3390/pharmaceutics14112515
Pharmaceutics, Vol. 14, Num. 11 (November 2022) , art. 2515
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4.
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8 p, 1.2 MB |
SGnn : A Web Server for the Prediction of Prion-Like Domains Recruitment to Stress Granules Upon Heat Stress
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Iglesias, Valentin (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Santos, Jaime (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Santos-Suárez, Juan (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pintado-Grima, Carlos (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Proteins bearing prion-like domains (PrLDs) are essential players in stress granules (SG) assembly. Analysis of data on heat stress-induced recruitment of yeast PrLDs to SG suggests that this propensity might be connected with three defined protein biophysical features: aggregation propensity, net charge, and the presence of free cysteines. [...]
2021 - 10.3389/fmolb.2021.718301
Frontiers in Molecular Biosciences, Vol. 8 (August 2021) , art. 718301
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194 p, 7.0 MB |
Bioinformatic analysis on the determinants of protein aggregation and conformational conversion
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Iglesias Mas, Valentín ;
Ventura Zamora, Salvador, dir.
L'agregació de proteïnes ha passat de ser gairebé una curiositat biofísica sense major interès a un dels camps més actius de la recerca, especialment des que es va esbrinar que podia ser la causa de diverses malalties en humans. [...]
La agregación de proteínas ha pasado de ser prácticamente una curiosidad biofísica sin mayor interés a uno de los campos más activos de la investigación, especialmente desde que se dilucidó como el causante de diversas enfermedades en humanos. [...]
Protein aggregation has moved from being an almost neglected biophysical curiosity to a central research field mostly due to aggregating proteins causing debilitating conditions in humans. The aggregation propensity of polypeptidic sequences is primarily dictated by their amino acid sequence, which delimits the possible interactions between amino acids. [...]
2021
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14 p, 2.8 MB |
Critical assessment of protein intrinsic disorder prediction
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Necci, Marco (University of Padua. Department of Biomedical Sciences) ;
Piovesan, Damiano (University of Padua. Department of Biomedical Sciences) ;
Hoque, M. T. (University of New Orleans. Computer Science) ;
Walsh, Ian (Agency for Science, Technology and Research. Bioprocessing Technology Institute) ;
Iqbal, Sumaiya (Broad Institute of MIT and Harvard. Center for Psychiatric Research) ;
Vendruscolo, Michele (University of Cambridge. Centre for Misfolding Diseases. Department of Chemistry) ;
Sormanni, Pietro (University of Cambridge. Centre for Misfolding Diseases. Department of Chemistry) ;
Wang, Chen (Columbia University. Department of Medicine) ;
Raimondi, Daniele (ESAT-STADIUS. KU Leuven) ;
Sharma, Ronesh (Fiji National University) ;
Zhou, Yaoqi (Griffith University. Institute for Glycomics and School of Information and Communication Technology) ;
Litfin, Thomas (Griffith University. Institute for Glycomics and School of Information and Communication Technology) ;
Galzitskaya, Oxxana Valerianovna (Russian Academy of Sciences. Institute of Theoretical and Experimental Biophysics) ;
Lobanov, Michail Yu (Russian Academy of Sciences. Institute of Protein Research) ;
Vranken, Wim (Vrije Universiteit Brussel. Interuniversity Institute of Bioinformatics in Brussels) ;
Wallner, Björn (Linköping University. Department of Physics, Chemistry and Biology) ;
Mirabello, Claudio (Linköping University. Department of Physics, Chemistry and Biology) ;
Malhis, Nawar (University of British Columbia. Michael Smith Laboratories) ;
Dosztányi, Zsuzsanna (Eötvös Loránd University. Department of Biochemistry) ;
Erdős, Gábor (Eötvös Loránd University. Department of Biochemistry) ;
Mészáros, Bálint (European Molecular Biology Laboratory. Structural and Computational Biology Unit) ;
Gao, Jianzhao (Nankai University. School of Mathematical Sciences and LPMC) ;
Wang, Kui (Nankai University. School of Mathematical Sciences and LPMC) ;
Hu, Gang (Nankai University. School of Statistics and Data Science) ;
Wu, Zhonghua (Nankai University. School of Mathematical Sciences and LPMC) ;
Sharma, Alok (University of the South Pacific. School of Engineering and Physics) ;
Hanson, Jack (Griffith University. School of Engineering and Built Environment. Signal Processing Laboratory Griffith University. School of Engineering and Built Environment. Signal Processing Laboratory Signal Processing Laboratory. School of Engineering and Built Environment. Griffith University) ;
Callebaut, Isabelle (Sorbonne Université. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie. Muséum National d'Histoire Naturelle) ;
Bitard-Feildel, Tristan (Sorbonne Université. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie. Muséum National d'Histoire Naturelle) ;
Orlando, Gabriele (VIB-KU Leuven. Switch Laboratorium.) ;
Peng, Zhenling (Tianjin University. Center for Applied Mathematics) ;
Xu, Jinbo (Toyota Technological Institute at Chicago) ;
Wang, Sheng (Toyota Technological Institute at Chicago) ;
Jones, David T. (University College London) ;
Cozzetto, Domenico (University College London) ;
Meng, Fanchi (University of Alberta. Department of Electrical and Computer Engineering) ;
Yan, Jing (University of Alberta. Department of Electrical and Computer Engineering) ;
Gsponer, Jörg (University of British Columbia. Michael Smith Laboratories) ;
Cheng, Jianlin (University of Missouri. Department of Electrical Engineering and Computer Science) ;
Wu, Tianqi (University of Missouri. Department of Electrical Engineering and Computer Science) ;
Kurgan, Lukasz (Virginia Commonwealth University. Department of Computer Science) ;
Promponas, Vasilis J. (University of Cyprus. Department of Biological Sciences. Bioinformatics Research Laboratory) ;
Tamana, Stella (University of Cyprus. Department of Biological Sciences. Bioinformatics Research Laboratory) ;
Marino-Buslje, Cristina (Fundación Instituto Leloir (Buenos Aires, Argentina)) ;
Martínez-Pérez, Elisabeth (Fundación Instituto Leloir (Buenos Aires, Argentina)) ;
Chasapi, Anastasia (Centre for Research & Technology Hellas. Chemical Process & Energy Resources Institute) ;
Ouzounis, Christos (Centre for Research & Technology Hellas. Chemical Process & Energy Resources Institute) ;
Dunker, A. Keith (Indiana University School of Medicine. Center for Computational Biology and Bioinformatics) ;
Kajava, Andrey V (University of Montpellier. Centre de Recherche en Biologie cellulaire de Montpellier) ;
Leclercq, Jeremy Y. (University of Montpellier. Centre de Recherche en Biologie cellulaire de Montpellier) ;
Aykac-Fas, Burcu (Danish Cancer Society Research Center) ;
Lambrughi, Matteo (Danish Cancer Society Research Center) ;
Maiani, Emiliano (Danish Cancer Society Research Center) ;
Papaleo, Elena (Danish Cancer Society Research Center) ;
Chemes, Lucía Beatriz (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas) ;
Álvarez, Lucía (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas) ;
González-Foutel, Nicolás S. (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas) ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Pujols Pujol, Jordi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Palopoli, Nicolas (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología) ;
Benítez, Guillermo I (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología) ;
Parisi, Gustavo (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología) ;
Bassot, Claudio (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory) ;
Elofsson, Arne (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory) ;
Govindarajan, Sudha (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory) ;
Lamb, John (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory) ;
Salvatore, Marco (Copenhagen University. Department of Biology) ;
Hatos, András (Università di Padova. Dipartimento di Scienze Biomediche) ;
Monzon, Alexander Miguel (Università di Padova. Dipartimento di Scienze Biomediche) ;
Bevilacqua, Martina (Università di Padova. Dipartimento di Scienze Biomediche) ;
Mičetić, Ivan (Università di Padova. Dipartimento di Scienze Biomediche) ;
Minervini, Giovanni (Università di Padova. Dipartimento di Scienze Biomediche) ;
Paladin, Lisanna (Università di Padova. Dipartimento di Scienze Biomediche) ;
Quaglia, Federica (Università di Padova. Dipartimento di Scienze Biomediche) ;
Leonardi, Emanuela (Università di Padova) ;
Davey, Norman E. (The Institute of Cancer Research. Chelsea) ;
Horvath, Tamas (Research Centre for Natural Sciences. Institute of Enzymology) ;
Kovacs, Orsolya Panna (Research Centre for Natural Sciences. Institute of Enzymology) ;
Murvai, Nikoletta (Research Centre for Natural Sciences. Institute of Enzymology) ;
Pancsa, Rita (Research Centre for Natural Sciences. Institute of Enzymology) ;
Schad, Eva (Research Centre for Natural Sciences. Institute of Enzymology) ;
Szabo, Beata (Research Centre for Natural Sciences. Institute of Enzymology) ;
Tantos, Agnes (Research Centre for Natural Sciences. Institute of Enzymology) ;
Macedo-Ribeiro, Sandra (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Manso, Jose Antonio (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Barbosa Pereira, Pedro José (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Davidović, Radoslav (University of Belgrade. Vinča Institute of Nuclear Sciences - National Institute of thе Republic of Serbia.) ;
Veljkovic, Nevena (University of Belgrade. Vinča Institute of Nuclear Sciences - National Institute of thе Republic of Serbia.) ;
Hajdu-Soltész, Borbála (Eötvös Loránd University. Department of Biochemistry) ;
Pajkos, Mátyás (Eötvös Loránd University. Department of Biochemistry) ;
Szaniszló, Tamás (Eötvös Loránd University. Department of Biochemistry) ;
Guharoy, Mainak (Vrije Universiteit Brussel. Structural Biology Brussels) ;
Lazar, Tamas (Vrije Universiteit Brussel. Structural Biology Brussels) ;
Macossay-Castillo, Mauricio (Vrije Universiteit Brussel. Structural Biology Brussels) ;
Tompa, Peter (Vrije Universiteit Brussel. Structural Biology Brussels) ;
Tosatto, Silvio (University of Padua. Department of Biomedical Sciences)
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. [...]
2021 - 10.1038/s41592-021-01117-3
Nature Methods, Vol. 18 (May 2021) , p. 472-481
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