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

UniProt: a hub for protein information

Autor: Ursula Hinz, Prudence Mutowo, Laure Verbregue, Weizhong Li, Nadine Gruaz-Gumowski, Chantal Hulo, Hermann Zellner, Shyamala Sundaram, P Lemercier, Guoying Qi, Parit Bansal, Tony Sawford, Sebastien Gehant, Delphine Baratin, Francesco Fazzini, Monica Pozzato, Séverine Duvaud, Lai-Su L. Yeh, Nicole Redaschi, Emma Hatton-Ellis, Darren A. Natale, Damien Lieberherr, Luis Figueira, Bernd Roechert, Borisas Bursteinas, Gayatri Chavali, Brigitte Boeckmann, Cristina Casal-Casas, Baris E. Suzek, Cathy H. Wu, Paul Gane, Ghislaine Argoud-Puy, Klemens Pichler, Rachael P. Huntley, Sangya Pundir, Alan Bridge, Edouard de Castro, Benoit Bely, Kristian B. Axelsen, Emmanuel Boutet, Andre Stutz, Penelope Garmiri, Christian J. A. Sigrist, John S. Garavelli, Rolf Apweiler, Peter B. McGarvey, Patrick Masson, Maria Jesus Martin, K Sonesson, Xavier Watkins, Ioannis Xenarios, Vladimir Volynkin, Hamish McWilliam, Mark Bingley, Guillaume Keller, Hongzhan Huang, Rabie Saidi, Sylvain Poux, Tunca Doğan, Yuqi Wang, Diego Poggioli, Rodrigo Lopez, Alistair MacDougall, Kati Laiho, Qinghua Wang, W Liu, Carlos Bonilla, Duncan Legge, C. R. Vinayaka, Anne Morgat, Thierry Lombardot, Jerven Bolleman, Nevila Nouspikel, Aleksandra Shypitsyna, Emanuele Alpi, Yongxing Chen, Anne Lise Veuthey, Andrew Nightingale, Béatrice A. Cuche, Alex Bateman, Ramona Britto, Alan Wilter Sousa da Silva, Jie Luo, Lionel Breuza, Marie Claude Blatter, Elena Cibrian-Uhalte, Michel Schneider, Chuming Chen, Michele Magrane, L Famiglietti, Meher Shruti Yerramalla, Lydie Bougueleret, Vivienne Baillie Gerritsen, Anne Estreicher, Dolnide Dornevil, Catherine Rivoire, Jian Zhang, S Staehli, Andrew Peter Cowley, Tony Wardell, Ivo Pedruzzi, Andrea H. Auchincloss, Salvo Paesano, Elisabeth Gasteiger, Luis Pureza, Marc Feuermann, Leslie Arminski, Xavier D. Martin, Teresa Batista Neto, Steven Rosanoff, Florence Jungo, Sandra Orchard, Claire O'Donovan, Elisabeth Coudert, Ricardo Antunes, Sandrine Pilbout, Vicente Lara, Arnaud Gos, Reija Hieta, Manuela Pruess, Joanna Arganiska, Edward Turner, Maurizio De Giorgi, M Doche, Cecilia N. Arighi, Michael Tognolli, Leyla Jael Garcia Castro, Lucila Aimo

Publikováno v: Nucleic Acids Research

UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 c

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::429cad485e24854c12fb7ce51fdc3b2a
https://pubmed.ncbi.nlm.nih.gov/25348405

The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database

Autor: Lois T. Hunt, Leslie Arminski, John S. Garavelli, Robert J. Dodson, Daniel H. Haft, Christopher R. Marzec, Kathryn E. Sidman, Bruce C. Orcutt, Geetha Y. Srinivasarao, Robert S. Ledley, Akira Tsugita, David G. George, Lai-Su L. Yeh, Winona C. Barker

Publikováno v: Nucleic Acids Research. 25:24-27

From its origin, the PIR has aspired to support research in computational biology and genomics through the compilation of a comprehensive, quality controlled and well-organized protein sequence information resource. The resource originated with the p

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::df804ed4b3f1ad0a941ed0431f154643
https://doi.org/10.1093/nar/25.1.24

Community annotation in biology

Autor: Cathy H. Wu, Raja Mazumder, Lai-Su L. Yeh, Jessica Anne Ecalnir Julio, Darren A. Natale

Publikováno v: Biology Direct
Biology Direct, Vol 5, Iss 1, p 12 (2010)

Attempts to engage the scientific community to annotate biological data (such as protein/gene function) stored in databases have not been overly successful. There are several hypotheses on why this has not been successful but it is not clear which of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::732e4a27d477ece7921461e0edf71eae
https://pubmed.ncbi.nlm.nih.gov/20167071

UniProt: the Universal Protein knowledgebase

Autor: Cathy H. Wu, Winona C. Barker, Serenella Ferro, Rolf Apweiler, Brigitte Boeckmann, Rodrigo Lopez, Claire O'Donovan, Elisabeth Gasteiger, Amos Marc Bairoch, Maria Jesus Martin, Hongzhan Huang, Nicole Redaschi, Lai-Su L. Yeh, Darren A. Natale, Michele Magrane

Publikováno v: Nucleic Acids Research, Vol. 32, No Database issue (2004) pp. D115-9
Scopus-Elsevier

To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebas

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0bf9c251ba7286fd7da174ab3880d204
https://archive-ouverte.unige.ch/unige:40342