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HINT: a database of annotated protein-protein interactions and their homologs

View Article: PubMed Central - PubMed

ABSTRACT

Despite the abundance of protein-protein interaction databases currently available online, a source that identifies and lists similar interactions in different species is lacking. The Homologous Interactions (HINT) database is such a collection of protein-protein interactions and their homologs in one or more species. The interactions and their homologs are annotated with Eukaryotic Cluster of Orthologous Groups (KOG) IDs, InterPro domains, Gene Ontology (GO) terminology and Protein Data Bank (PDB) structures. HINT is available as an interactive Web server at http://helix.protein.osaka-u.ac.jp/hint/.

No MeSH data available.


Web Interface of the Database of Homologous Interactions with interaction details and GO, InterPro and KOG annotations of the interacting proteins. Also shown is a graph of the homologs with the query interaction in yellow, InterPro domains of the interacting proteins in blue and the homologs of the proteins colored differently with varying hit scores, similar to BLAST results10. The species in which the homolog is found is given by a 2 letter code as given in Table 1. If the interaction is an ortholog or a paralog of the query interaction, it is indicated by an ‘O’ or a ‘P’ along side each homolog. Clicking on the ‘+’ gives further details of the homolog such as E-value, percent identity, hit score and KOG, where available. Tool tips are provided in various places.
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f2-1_21: Web Interface of the Database of Homologous Interactions with interaction details and GO, InterPro and KOG annotations of the interacting proteins. Also shown is a graph of the homologs with the query interaction in yellow, InterPro domains of the interacting proteins in blue and the homologs of the proteins colored differently with varying hit scores, similar to BLAST results10. The species in which the homolog is found is given by a 2 letter code as given in Table 1. If the interaction is an ortholog or a paralog of the query interaction, it is indicated by an ‘O’ or a ‘P’ along side each homolog. Clicking on the ‘+’ gives further details of the homolog such as E-value, percent identity, hit score and KOG, where available. Tool tips are provided in various places.

Mentions: 11103 of the 45840 interactions (24%) have one or more homologs in HINT. Table 1 shows the distribution of the homologs across species. The web interface can be used to search interactions using various identifiers such as SwissProt Accession numbers, PIR IDs, GenBank Accession numbers, RefSeq IDs or descriptions of the interacting proteins. An interaction of interest can be selected from the results of the search to obtain detailed information about it. Figure 2 shows a snapshot of the Interactions web page. The homologs of the interaction selected are shown in graphical form as well as tabular form and sorted according to the score of the protein hits, with the best hits shown first. The graphical form helps the user to visualize the regions and domains that are common among the proteins of the selected interaction and those of the homologous interactions. The tabular form gives details about the E-values and the percent identity given by PSIBlast. Further details about the usage of the web interface are provided in the form of an online Help document.


HINT: a database of annotated protein-protein interactions and their homologs
Web Interface of the Database of Homologous Interactions with interaction details and GO, InterPro and KOG annotations of the interacting proteins. Also shown is a graph of the homologs with the query interaction in yellow, InterPro domains of the interacting proteins in blue and the homologs of the proteins colored differently with varying hit scores, similar to BLAST results10. The species in which the homolog is found is given by a 2 letter code as given in Table 1. If the interaction is an ortholog or a paralog of the query interaction, it is indicated by an ‘O’ or a ‘P’ along side each homolog. Clicking on the ‘+’ gives further details of the homolog such as E-value, percent identity, hit score and KOG, where available. Tool tips are provided in various places.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036632&req=5

f2-1_21: Web Interface of the Database of Homologous Interactions with interaction details and GO, InterPro and KOG annotations of the interacting proteins. Also shown is a graph of the homologs with the query interaction in yellow, InterPro domains of the interacting proteins in blue and the homologs of the proteins colored differently with varying hit scores, similar to BLAST results10. The species in which the homolog is found is given by a 2 letter code as given in Table 1. If the interaction is an ortholog or a paralog of the query interaction, it is indicated by an ‘O’ or a ‘P’ along side each homolog. Clicking on the ‘+’ gives further details of the homolog such as E-value, percent identity, hit score and KOG, where available. Tool tips are provided in various places.
Mentions: 11103 of the 45840 interactions (24%) have one or more homologs in HINT. Table 1 shows the distribution of the homologs across species. The web interface can be used to search interactions using various identifiers such as SwissProt Accession numbers, PIR IDs, GenBank Accession numbers, RefSeq IDs or descriptions of the interacting proteins. An interaction of interest can be selected from the results of the search to obtain detailed information about it. Figure 2 shows a snapshot of the Interactions web page. The homologs of the interaction selected are shown in graphical form as well as tabular form and sorted according to the score of the protein hits, with the best hits shown first. The graphical form helps the user to visualize the regions and domains that are common among the proteins of the selected interaction and those of the homologous interactions. The tabular form gives details about the E-values and the percent identity given by PSIBlast. Further details about the usage of the web interface are provided in the form of an online Help document.

View Article: PubMed Central - PubMed

ABSTRACT

Despite the abundance of protein-protein interaction databases currently available online, a source that identifies and lists similar interactions in different species is lacking. The Homologous Interactions (HINT) database is such a collection of protein-protein interactions and their homologs in one or more species. The interactions and their homologs are annotated with Eukaryotic Cluster of Orthologous Groups (KOG) IDs, InterPro domains, Gene Ontology (GO) terminology and Protein Data Bank (PDB) structures. HINT is available as an interactive Web server at http://helix.protein.osaka-u.ac.jp/hint/.

No MeSH data available.