Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Autor: Denise Kühnert, Vincent Navratil, Roman Martin, Marius Welzel, Franziska Hufsky, Guillermo Rangel-Pineros, Marie Hoffmann, Julian Matschinske, Robert D. Finn, Manja Marz, Hannah F. Löchel, Georges Hattab, Jan Baumbach, Stefan Hoops, Alice C. McHardy, Pedro Mendes, Kevin Lamkiewicz, Niko Beerenwinkel, Ioanna Kalvari, Joshua B Singer, Maria Jesus Martin, David Robertson, Jaina Mistry, Alexandre Almeida, Chris Upton, Markus List, Sara Chuguransky, Cecilia N. Arighi, Oliver Drechsel, Nicole Redaschi, Dominik Heider, Alex Bateman, Lorna Richardson, Christian Brandt, Pieter Libin, Adrian Fritz, Anton I. Petrov, Lars Kaderali, Knut Reinert, Lowri Williams, Max von Kleist, Áine O'Toole, Abdel Aouacheria, Martin Hölzer, Nancy Ontiveros-Palacios, Susanne Reimering, Kristof Theys, Stephan Fuchs, Anne-Christin Hauschild, Sepideh Sadegh, Gorka Lasso, Marco Cacciabue, Eric P. Nawrocki, Alejandro Reyes, Renó Kmiecinski

Publikováno v: Briefings in Bioinformatics
Briefings in Bioinformatics, Oxford University Press (OUP), 2020, ⟨10.1093/bib/bbaa232⟩
Preprints
Briefings in bioinformatics
England
Hufsky, F, Lamkiewicz, K, Almeida, A, Aouacheria, A, Arighi, C, Bateman, A, Baumbach, J, Beerenwinkel, N, Brandt, C, Cacciabue, M, Chuguransky, S, Drechsel, O, Finn, R D, Fritz, A, Fuchs, S, Hattab, G, Hauschild, A-C, Heider, D, Hoffmann, M, Hölzer, M, Hoops, S, Kaderali, L, Kalvari, I, von Kleist, M, Kmiecinski, R, Kühnert, D, Lasso, G, Libin, P, List, M, Löchel, H F, Martin, M J, Martin, R, Matschinske, J, McHardy, A C, Mendes, P, Mistry, J, Navratil, V, Nawrocki, E P, O'Toole, A N, Ontiveros-Palacios, N, Petrov, A I, Rangel-Pineros, G, Redaschi, N, Reimering, S, Reinert, K, Reyes, A, Richardson, L, Robertson, D L, Sadegh, S, Singer, J B, Theys, K, Upton, C, Welzel, M, Williams, L & Marz, M 2021, ' Computational strategies to combat COVID-19 : useful tools to accelerate SARS-CoV-2 and coronavirus research ', Briefings in Bioinformatics, vol. 22, no. 2, pp. 642-663 . https://doi.org/10.1093/bib/bbaa232
Briefings in Bioinformatics, 22 (2)
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Consejo Nacional de Investigaciones Científicas y Técnicas
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Briefings in Bioinformatics, 2020, ⟨10.1093/bib/bbaa232⟩

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causesthe infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformaticstools des

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7cc1ebc9849708c6b19e128f12d7c8fc

The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam

Autor: Penelope Coggill, Marco Punta, Robert D. Finn, Milton H. Saier, Jaina Mistry, Åke Västermark, Zachary Chiang

Publikováno v: Briefings in bioinformatics, vol 16, iss 5
Briefings in Bioinformatics
Chiang, Z; Vastermark, A; Punta, M; Coggill, PC; Mistry, J; Finn, RD; et al.(2014). The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. Briefings in Bioinformatics, 16(5), 865-872. doi: 10.1093/bib/bbu053. UC San Diego: Retrieved from: http://www.escholarship.org/uc/item/0k22s33f

Transport systems comprise roughly 10% of all proteins in a cell, playing critical roles in many processes. Improving and expanding their classification is an important goal that can affect studies ranging from comparative genomics to potential drug

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1207d941df87091ba71b25f7b8df8b84
https://doi.org/10.1093/bib/bbu053

InterPro in 2017-beyond protein family and domain annotations

Autor: Ian Sillitoe, Hsin-Yu Chang, Sara El-Gebali, Siew Yit Young, Youngmi Park, Jaina Mistry, Sebastien Pesseat, Narmada Thanki, Cathy H. Wu, Alan Bridge, Ioannis Xenarios, Ben Smithers, Simon C. Potter, Silvano Squizzato, Nicole Redaschi, Darren A. Natale, Paul Thomas, David R. Haft, Ivica Letunic, Granger G. Sutton, Silvio C. E. Tosatto, Gift Nuka, Gemma L. Holliday, Alex L. Mitchell, Teresa K. Attwood, Marco Necci, Neil D. Rawlings, Shennan Lu, Julian Gough, Alex Bateman, Patricia C. Babbitt, Lorna Richardson, Lai-Su L. Yeh, Amaia Sangrador-Vegas, Zsuzsanna Dosztányi, Rodrigo Lopez, Damiano Piovesan, Matthew Fraser, Aron Marchler-Bauer, Robert D. Finn, Peer Bork, Christine A. Orengo, Xiaosong Huang, Huaiyu Mi, Hongzhan Huang, Christian J. A. Sigrist, Catherine Rivoire

Publikováno v: Nucleic acids research, vol 45, iss D1
Finn, R D, Attwood, T K, Babbitt, P C, Bateman, A, Bork, P, Bridge, A J, Chang, H Y, Dosztanyi, Z, El-Gebali, S, Fraser, M, Gough, J, Haft, D, Holliday, G L, Huang, H, Huang, X, Letunic, I, Lopez, R, Lu, S, Marchler-Bauer, A, Mi, H, Mistry, J, Natale, D A, Necci, M, Nuka, G, Orengo, C A, Park, Y, Pesseat, S, Piovesan, D, Potter, S C, Rawlings, N D, Redaschi, N, Richardson, L, Rivoire, C, Sangrador-Vegas, A, Sigrist, C, Sillitoe, I, Smithers, B, Squizzato, S, Sutton, G, Thanki, N, Thomas, P D, Tosatto, S C E, Wu, C H, Xenarios, I, Yeh, L S, Young, S Y & Mitchell, A L 2016, ' InterPro in 2017-beyond protein family and domain annotations ', Nucleic Acids Research, vol. 45, no. D1, pp. D190-D199 . https://doi.org/10.1093/nar/gkw1107
Finn, R D, Attwood, T K, Babbitt, P C, Bateman, A, Bork, P, Bridge, A J, Chang, H-Y, Dosztányi, Z, El-Gebali, S, Fraser, M, Gough, J, Haft, D, Holliday, G L, Huang, H, Huang, X, Letunic, I, Lopez, R, Lu, S, Marchler-Bauer, A, Mi, H, Mistry, J, Natale, D A, Necci, M, Nuka, G, Orengo, C A, Park, Y, Pesseat, S, Piovesan, D, Potter, S C, Rawlings, N D, Redaschi, N, Richardson, L, Rivoire, C, Sangrador-Vegas, A, Sigrist, C, Sillitoe, I, Smithers, B, Squizzato, S, Sutton, G, Thanki, N, Thomas, P D, Tosatto, S C E, Wu, C H, Xenarios, I, Yeh, L-S, Young, S-Y & Mitchell, A L 2017, ' InterPro in 2017-beyond protein family and domain annotations ', Nucleic acids research, vol. 45, no. D1, pp. D190-D199 . https://doi.org/10.1093/nar/gkw1107
Nucleic Acids Research

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::09ef53ce889ada380b316e2da5a8c210
http://hdl.handle.net/11577/3230382

Homology-Based Annotation of Large Protein Datasets

Autor: Marco, Punta, Jaina, Mistry

Publikováno v: Methods in molecular biology (Clifton, N.J.). 1415

Advances in DNA sequencing technologies have led to an increasing amount of protein sequence data being generated. Only a small fraction of this protein sequence data will have experimental annotation associated with them. Here, we describe a protoco

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::cea1cdbc2f1d71d823462a262d68b3d1
https://pubmed.ncbi.nlm.nih.gov/27115632

Homology-Based Annotation of Large Protein Datasets

Autor: Marco Punta, Jaina Mistry

Publikováno v: DATA MINING TECHNIQUES FOR THE LIFE SCIENCES
Carugo, O and Eisenhaber, F. DATA MINING TECHNIQUES FOR THE LIFE SCIENCES, 1415, HUMANA PRESS INC, pp.153-176, 2016, Methods in Molecular Biology, 978-1-4939-3572-7; 978-1-4939-3570-3. ⟨10.1007/978-1-4939-3572-7_8⟩
Methods in Molecular Biology ISBN: 9781493935703

International audience; Advances in DNA sequencing technologies have led to an increasing amount of protein sequence data being generated. Only a small fraction of this protein sequence data will have experimental annotation associated with them. Her

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::96dac742fc4f7d7382d06d36c74a4dbd
https://hal.science/hal-01528505