The InterPro Database, 2003 brings increased coverage and new features

By Nicola J. Mulder, Rolf Apweiler, T. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, M. Biswas, Paul Bradley, Peer Bork and 27 more. Nucleic Acids Res., 2003

727 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dacc0018d0a0c45d93599751e53c91f88fcd45b8

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Citations in the corpus

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology (2004, background): “These mappings are shared on the EBI FTP site: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/.”
GlobPlot: exploring protein sequences for globularity and disorder (2003, methodology): “The SMART/Pfam prediction substantially increases the plotting time, but is set to 'on' by default because it is a very informative feature.”
ProFunc: a server for predicting protein function from 3D structure (2005, methodology): “Finally, the target sequence is scanned against the numerous motifs, patterns, fingerprints and hidden Markov models (HMMs) of Interpro ( 8 ) by running InterProScan (9).”
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark (2005, methodology): “( 3 ) Because divergent sequences cannot be aligned accurately without using structural information as a guide, Uniprot sequences of unknown structure are only included in the alignment if they share 40% identity with at least one PDB sequence.”
The Proteomics Protocols Handbook (2005, background): “Fractionation with X-114 allows subfractionation of peripheral vs integral membrane proteins (32,33), and lends further flexibility to fractionation goals.”
GeneSilico protein structure prediction meta-server (2003, methodology): “The HMMPFAM tool for the primary structure analysis (identification of PFAM domains) (12).”
SWISS-MODEL: an automated protein homology-modeling server (2003, methodology): “In an ongoing project, 3D models built by SWISS-MODEL are integrated into the INTERPRO (35) database.”
PIRSF Family Classification System for Protein Functional and Evolutionary Analysis (2006, background): “…as family relationships at the full-length protein, domain, and motif levels with direct mapping and links to other family, function, and structure classifi cation schemes, such as Pfam and InterPro (Mulder et al 2003); and (iv) graphical display: domain architecture of seed members or all members.”
ArrayExpress—a public repository for microarray gene expression data at the EBI (2004, methodology): “The ArrayExpress data warehouse [which is based on the BioMart technology (11)] supports queries on gene attributes, such as gene names, gene function (GO annotations) or information on which family a gene belongs to or the motifs and domains it contains (InterPro terms), and on sample properties.”
The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website (2004, background): “Other information is held to provide links to web resources such as Ensembl (Birney et al , 2004), Pfam (Bateman et al , 2004), InterPro (Mulder et al , 2003) and OMIM (Wheeler et al , 2004).”
Human MicroRNA Targets (2004, methodology): “and domain annotations from InterPro (Mulder et al. 2003).”
PIRSF: family classification system at the Protein Information Resource (2004, background): “The algorithm, PIRSF-Scan, has been incorporated into the InterProScan program.”
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004, unknown): “3.1 (Mulder et al. 2003).”
SCOP database in 2004: refinements integrate structure and sequence family data (2004, background): “A project has started during the past year that aims to rationalize and integrate the SCOP information with the data about protein families housed by prominent sequence and structural databases, including InterPro (8), Pfam (9), CATH (10) and MSD (11).”
The Universal Protein Resource (UniProt) (2004, methodology): “Approximately 80% of all UniProt Knowledgebase records are classiﬁed according to their InterPro domains and familes.”
Recent improvements to the PROSITE database (2004, background): “InterPro ( 8 ) provides an integrated view of several domain databases and offers a large choice of methods to identify conserved regions.”