Recent improvements to the PROSITE database

By Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, Amos Bairoch. Nucleic Acids Res., 2004

471 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/01ae1d46bb1e3d5da2754f25dcfaaed58639ca61

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Burkhard Rost
2. Janet M. Thornton
3. Roman A. Laskowski
4. David S. Wishart
5. Victor V. Chistyakov
6. Amos Bairoch
7. Rodrigo Lopez
8. Anchi Guo

Citations in the corpus

• BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark (2005, background): “The region shown in the multiple alignment includes the putative AMP-binding domain signature; a region rich in glycine, serine and threonine, followed by a conserved lysine, as defined in the PROSITE database 55 (PDOC00427).”
• InterProScan: protein domains identifier (2005, unknown): “PROSITE (12) ScanRegExp + ProfileScan (13)”
• A Database of Bacterial Lipoproteins (DOLOP) with Functional Assignments to Predicted Lipoproteins (2006, background): “It is important to mention here that the PS00013 signature provided by Prosite (25) was one of the first available prediction algorithms to identify bacterial lipoproteins.”
• ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins (2006, background): “Protein databases can be randomized (reversed or shuffled) to evaluate user pattern significance (8).”
• PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids (2004, methodology): “As before, a detailed analysis of the secondary structure motifs is provided, via PROMOTIF (10), and any valid PROSITE patterns (11) contained within the sequence are mapped to the 3D structure (12) via RasMol.”
• The ProDom database of protein domain families: more emphasis on 3D (2004, methodology): “This comprehensiveness makes ProDom a unique resource usefully complementing expert derived databases, such as PROSITE (4), PFAM (5) or SMART (6), thereby helping to sustain the rapid growth of InterPro (7,8).”
• The Universal Protein Resource (UniProt) (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (14), PROSITE (15), PRINTS (16), ProDom (17), SMART (18), PIRSF (19), Superfamily (20) and TIGRFAMs (21).”
• TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes (2005, methodology): “The automatically assigned domains, which are linked to the corresponding Pfam, SMART and PROSITE entries, are meant to complement the manually annotated domains, many of which are based on functional studies reported in the original literature.”
• BASys: a web server for automated bacterial genome annotation (2005, methodology): “protein family analysis with Pfam (15), sequence motif analysis with PROSITE ( 16 ), signal peptide domain prediction with PredictSPTM (J. Cruz, unpublished data), and predicted structure with PSIPRED If the sequence to a sequence represented in the PDB database, then BASys may use HOMODELLER (X. Do”
• The PROSITE database (2005, methodology): “As a more detailed description of the PROSITE database has already been provided in previous publications (1,2), this paper will only focus on recent developments that have taken place during 40 the last 2 years.”
• Pfam: clans, web tools and services (2005, unknown): “Influenced by SMART (12) and PROSITE ( 13 ), the graphical representation of domains has been updated on the website (Table 2). In addition to each domain having more of a 3D look, additional sequence features are now visualized.”
• UniProt: the Universal Protein knowledgebase (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF (16), Superfamily (17) and TIGRFAMs (18).”