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  1. Article ; Online: A potential role for integrins in host cell entry by SARS-CoV-2.

    Sigrist, Christian Ja / Bridge, Alan / Le Mercier, Philippe

    Antiviral research

    2020  Volume 177, Page(s) 104759

    MeSH term(s) Animals ; Betacoronavirus/metabolism ; COVID-19 ; Coronavirus Infections/physiopathology ; Coronavirus Infections/virology ; Drug Delivery Systems ; Host-Pathogen Interactions/physiology ; Humans ; Integrins/metabolism ; Pandemics ; Pneumonia, Viral/physiopathology ; Pneumonia, Viral/virology ; Protein Binding ; Protein Interaction Domains and Motifs ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Virus Internalization
    Chemical Substances Integrins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-03-01
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 306628-9
    ISSN 1872-9096 ; 0166-3542
    ISSN (online) 1872-9096
    ISSN 0166-3542
    DOI 10.1016/j.antiviral.2020.104759
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1627: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  3. Article ; Online: A potential role for integrins in host cell entry by SARS-CoV-2

    Sigrist, Christian JA / Bridge, Alan / Le Mercier, Philippe

    Antiviral Research

    2020  Volume 177, Page(s) 104759

    Keywords Pharmacology ; Virology ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 306628-9
    ISSN 1872-9096 ; 0166-3542
    ISSN (online) 1872-9096
    ISSN 0166-3542
    DOI 10.1016/j.antiviral.2020.104759
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article: PROSITE, a protein domain database for functional characterization and annotation

    Sigrist, Christian J.A / Cerutti, Lorenzo / de Castro, Edouard / Langendijk-Genevaux, Petra S / Bulliard, Virginie / Bairoch, Amos / Hulo, Nicolas

    Nucleic acids research. 2010 Jan., v. 38, no. suppl_1

    2010  

    Abstract: PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which ... ...

    Abstract PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 (~70%) are annotated with PROSITE descriptors using information from ProRule. In order to allow better functional characterization of domains, PROSITE developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/.
    Keywords amino acids ; databases ; nucleic acids ; sequence alignment ; zinc finger motif
    Language English
    Dates of publication 2010-01
    Size p. D161-D166.
    Document type Article
    ZDB-ID 186809-3
    ISSN 0301-5610 ; 0305-1048
    ISSN 0301-5610 ; 0305-1048
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: PeroxiBase: a database with new tools for peroxidase family classification

    Koua, Dominique / Cerutti, Lorenzo / Falquet, Laurent / Sigrist, Christian J.A / Theiler, Grégory / Hulo, Nicolas / Dunand, Christophe

    Nucleic acids research. 2009 Jan., v. 37, no. suppl_1

    2009  

    Abstract: Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. They use various peroxides as electron acceptors to catalyse a number of oxidative reactions ... ...

    Abstract Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. They use various peroxides as electron acceptors to catalyse a number of oxidative reactions and are present in almost all living organisms. We have created a peroxidase database (http://peroxibase.isb-sib.ch) that contains all identified peroxidase-encoding sequences (about 6000 sequences in 940 organisms). They are distributed between 11 superfamilies and about 60 subfamilies. All the sequences have been individually annotated and checked. PeroxiBase can be consulted using six major interlink sections 'Classes', 'Organisms', 'Cellular localisations', 'Inducers', 'Repressors' and 'Tissue types'. General documentation on peroxidases and PeroxiBase is accessible in the 'Documents' section containing 'Introduction', 'Class description', 'Publications' and 'Links'. In addition to the database, we have developed a tool to classify peroxidases based on the PROSITE profile methodology. To improve their specificity and to prevent overlaps between closely related subfamilies the profiles were built using a new strategy based on the silencing of residues. This new profile construction method and its discriminatory capacity have been tested and validated using the different peroxidase families and subfamilies present in the database. The peroxidase classification tool called PeroxiScan is accessible at the following address: http://peroxibase.isb-sib.ch/peroxiscan.php.
    Keywords databases ; nucleic acids ; peroxidase ; peroxides
    Language English
    Dates of publication 2009-01
    Size p. D261-D266.
    Document type Article
    ZDB-ID 186809-3
    ISSN 0301-5610 ; 0305-1048
    ISSN 0301-5610 ; 0305-1048
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: The 20 years of PROSITE

    Hulo, Nicolas / Bairoch, Amos / Bulliard, Virginie / Cerutti, Lorenzo / Cuche, Béatrice A / de Castro, Edouard / Lachaize, Corinne / Langendijk-Genevaux, Petra S / Sigrist, Christian J.A

    Nucleic acids research. 2008 Jan., v. 36, no. suppl_1

    2008  

    Abstract: PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which ... ...

    Abstract PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods. The latest version of PROSITE (release 20.19 of 11 September 2007) contains 1319 patterns, 745 profiles and 764 ProRules. Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match. PROSITE is available on the web at: http://www.expasy.org/prosite/.
    Keywords Internet ; amino acids ; methodology ; nucleic acids
    Language English
    Dates of publication 2008-01
    Size p. D245-D249.
    Document type Article
    ZDB-ID 186809-3
    ISSN 0301-5610 ; 0305-1048
    ISSN 0301-5610 ; 0305-1048
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

    de Castro, Edouard / Sigrist, Christian J.A / Gattiker, Alexandre / Bulliard, Virginie / Langendijk-Genevaux, Petra S / Gasteiger, Elisabeth / Bairoch, Amos / Hulo, Nicolas

    Nucleic acids research. 2006 July 1, v. 34, no. suppl_2

    2006  

    Abstract: ScanProsite--http://www.expasy.org/tools/scanprosite/--is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For a number of PROSITE profiles, the tool now makes use of ProRules--context- ... ...

    Abstract ScanProsite--http://www.expasy.org/tools/scanprosite/--is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For a number of PROSITE profiles, the tool now makes use of ProRules--context-dependent annotation templates--to detect functional and structural intra-domain residues. The detection of those features enhances the power of function prediction based on profiles. Both user-defined sequences and sequences from the UniProt Knowledgebase can be matched against custom patterns, or against PROSITE signatures. To improve response times, matches of sequences from UniProtKB against PROSITE signatures are now retrieved from a pre-computed match database. Several output modes are available including simple text views and a rich mode providing an interactive match and feature viewer with a graphical representation of results.
    Keywords Internet ; amino acid sequences ; databases ; nucleic acids ; prediction ; proteins
    Language English
    Dates of publication 2006-0701
    Size p. W362-W365.
    Document type Article
    ZDB-ID 186809-3
    ISSN 0301-5610 ; 0305-1048
    ISSN 0301-5610 ; 0305-1048
    Database NAL-Catalogue (AGRICOLA)

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  8. Article: InterPro: the integrative protein signature database

    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

    Nucleic acids research. 2009 Jan., v. 37, no. suppl_1

    2009  

    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, ...

    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/).
    Keywords Internet ; computer software ; databases ; models ; nucleic acids ; protein-protein interactions ; proteins
    Language English
    Dates of publication 2009-01
    Size p. D211-D215.
    Document type Article
    ZDB-ID 186809-3
    ISSN 0301-5610 ; 0305-1048
    ISSN 0301-5610 ; 0305-1048
    Database NAL-Catalogue (AGRICOLA)

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  9. Article: New developments in the InterPro database

    Mulder, Nicola J / Apweiler, Rolf / Attwood, Teresa K / Bairoch, Amos / Bateman, Alex / Binns, David / Bork, Peer / Buillard, Virginie / Cerutti, Lorenzo / Copley, Richard / Courcelle, Emmanuel / Das, Ujjwal / Daugherty, Louise / Dibley, Mark / Finn, Robert / Fleischmann, Wolfgang / Gough, Julian / Haft, Daniel / Hulo, Nicolas /
    Hunter, Sarah / Kahn, Daniel / Kanapin, Alexander / Kejariwal, Anish / Labarga, Alberto / Langendijk-Genevaux, Petra S / Lonsdale, David / Lopez, Rodrigo / Letunic, Ivica / Madera, Martin / Maslen, John / McAnulla, Craig / McDowall, Jennifer / Mistry, Jaina / Mitchell, Alex / Nikolskaya, Anastasia N / Orchard, Sandra / Orengo, Christine / Petryszak, Robert / Selengut, Jeremy D / Sigrist, Christian J.A / Thomas, Paul D / Valentin, Franck / Wilson, Derek / Wu, Cathy H / Yeats, Corin

    Nucleic acids research. 2007 Jan., v. 35, no. suppl_1

    2007  

    Abstract: InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new ... ...

    Abstract InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html.
    Keywords Internet ; artificial intelligence ; databases ; nucleic acids ; proteins
    Language English
    Dates of publication 2007-01
    Size p. D224-D228.
    Document type Article
    ZDB-ID 186809-3
    ISSN 0301-5610 ; 0305-1048
    ISSN 0301-5610 ; 0305-1048
    Database NAL-Catalogue (AGRICOLA)

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