@article {46742,
	title = {HMMER web server: 2015 update.},
	journal = {Nucleic Acids Research},
	year = {2015},
	month = {2015 May 5},
	abstract = {<p>The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.</p>
},
	issn = {1362-4962},
	doi = {10.1093/nar/gkv397},
	author = {Finn, Robert D and Clements, Jody and Arndt, William and Miller, Benjamin L and Wheeler, Travis J and Schreiber, Fabian and Bateman, Alex and Eddy, Sean R}
}
@article {6887,
	title = {iPfam: a database of protein family and domain interactions found in the Protein Data Bank.},
	journal = {Nucleic acids research},
	volume = {42},
	year = {2014},
	month = {2014 Jan},
	pages = {D364-73},
	abstract = {The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level. Previously, the iPfam domain-domain interaction data was integrated within the Pfam database and website, but it has now been migrated to a separate database. This allows for independent development, improving data access and giving clearer separation between the protein family and interactions datasets. In addition to domain-domain interactions, iPfam has been expanded to include interaction data for domain bound small molecule ligands. Functional annotations are provided from source databases, supplemented by the incorporation of Wikipedia articles where available. iPfam (version 1.0) contains >9500 domain-domain and 15 500 domain-ligand interactions. The new website provides access to this data in a variety of ways, including interactive visualizations of the interaction data.},
	keywords = {Databases, Internet, Ligands, Protein, Protein Interaction Domains and Motifs, Protein Interaction Mapping, Protein Interaction Maps, Proteins, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkt1210},
	author = {Finn, Robert D and Miller, Benjamin L and Clements, Jody and Bateman, Alex}
}
