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2. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit more...

Published
2012
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Catalog

Books, media, physical & digital resources
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3. InterPro: the integrative protein signature database

Author

Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., and Yeats, Corin more...

Published
2009

4. Dasty2, an Ajax protein DAS client

Author

Jimenez, Rafael C., Quinn, Antony F., Garcia, Alexander, Labarga, Alberto, O'Neill, Kieran, Martinez, Fernando, Salazar, Gustavo A., and Hermjakob, Henning

Published
2008

5. PRIDE: new developments and new datasets

Author

Jones, Philip, Côté, Richard G., Cho, Sang Yun, Klie, Sebastian, Martens, Lennart, Quinn, Antony F., Thorneycroft, David, and Hermjakob, Henning

Published
2008

7. Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Author

Cusick Michael E, Cerami Ethan, Salwinski Lukasz, Nerothin Jason, Stümpflen Volker, Oesterheld Matthias, Chatr-aryamontri Andrew, Ceol Arnaud, Moore Susan, Salama John J, Sherman David, Tyers Mike, Wojcik Jérôme, Xenarios Ioannis, Bader Gary D, Vinod Nisha, Quinn Antony F, Aranda Bruno, Montecchi-Palazzi Luisa, Orchard Sandra, Kerrien Samuel, Vidal Marc, Gilson Michael, Armstrong John, Woollard Peter, Hogue Christopher, Eisenberg David, Cesareni Gianni, Apweiler Rolf, and Hermjakob Henning more...

Subjects
Biology (General), QH301-705.5
Abstract

Abstract Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. Results The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. Conclusion The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel. more...

Published
2007
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8. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, Yong, Siew-Yit, Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit more...

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces more...

Published
2017

9. InterPro: the integrative protein signature database

Author

Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., Yeats, Corin, Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., and Yeats, Corin more...

Abstract

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/) more...

Published
2017

10. MyDas, an Extensible Java DAS Server

Author

Salazar, Gustavo A., primary, García, Leyla J., additional, Jones, Philip, additional, Jimenez, Rafael C., additional, Quinn, Antony F., additional, Jenkinson, Andrew M., additional, Mulder, Nicola, additional, Martin, Maria, additional, Hunter, Sarah, additional, and Hermjakob, Henning, additional more...

Published
2012
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11. Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Author

Kerrien, Samuel, primary, Orchard, Sandra, additional, Montecchi-Palazzi, Luisa, additional, Aranda, Bruno, additional, Quinn, Antony F, additional, Vinod, Nisha, additional, Bader, Gary D, additional, Xenarios, Ioannis, additional, Wojcik, Jérôme, additional, Sherman, David, additional, Tyers, Mike, additional, Salama, John J, additional, Moore, Susan, additional, Ceol, Arnaud, additional, Chatr-aryamontri, Andrew, additional, Oesterheld, Matthias, additional, Stümpflen, Volker, additional, Salwinski, Lukasz, additional, Nerothin, Jason, additional, Cerami, Ethan, additional, Cusick, Michael E, additional, Vidal, Marc, additional, Gilson, Michael, additional, Armstrong, John, additional, Woollard, Peter, additional, Hogue, Christopher, additional, Eisenberg, David, additional, Cesareni, Gianni, additional, Apweiler, Rolf, additional, and Hermjakob, Henning, additional more...

Published
2007
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12. InterPro in 2011: new developments in the family and domain prediction database

Author

Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, Yong, Siew-Yit, Hunter, Sarah, Jones, Philip, Mitchell, Alex, Apweiler, Rolf, Attwood, Teresa K., Bateman, Alex, Bernard, Thomas, Binns, David, Bork, Peer, Burge, Sarah, de Castro, Edouard, Coggill, Penny, Corbett, Matthew, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Fraser, Matthew, Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, McMenamin, Conor, Mi, Huaiyu, Mutowo-Muellenet, Prudence, Mulder, Nicola, Natale, Darren, Orengo, Christine, Pesseat, Sebastien, Punta, Marco, Quinn, Antony F., Rivoire, Catherine, Sangrador-Vegas, Amaia, Selengut, Jeremy D., Sigrist, Christian J. A., Scheremetjew, Maxim, Tate, John, Thimmajanarthanan, Manjulapramila, Thomas, Paul D., Wu, Cathy H., Yeats, Corin, and Yong, Siew-Yit more...

Abstract

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces more...

13. InterPro: the integrative protein signature database

Author

Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., Yeats, Corin, Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, Bork, Peer, Das, Ujjwal, Daugherty, Louise, Duquenne, Lauranne, Finn, Robert D., Gough, Julian, Haft, Daniel, Hulo, Nicolas, Kahn, Daniel, Kelly, Elizabeth, Laugraud, Aurélie, Letunic, Ivica, Lonsdale, David, Lopez, Rodrigo, Madera, Martin, Maslen, John, McAnulla, Craig, McDowall, Jennifer, Mistry, Jaina, Mitchell, Alex, Mulder, Nicola, Natale, Darren, Orengo, Christine, Quinn, Antony F., Selengut, Jeremy D., Sigrist, Christian J. A., Thimma, Manjula, Thomas, Paul D., Valentin, Franck, Wilson, Derek, Wu, Cathy H., and Yeats, Corin more...

Abstract

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/) more...