The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
New and continuing developments at PROSITE
Open accessAbstract
PROSITE (http://prosite.expasy.org/) 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, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. Here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. The latest version of PROSITE (release 20.85, of 30 August 2012) contains 1308 patterns, 1039 profiles and 1041 ProRules.
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Cites
PROSITE: a documented database using patterns and profiles as motif descriptors
Sigrist, C. J. A. (2002) · Briefings in Bioinformatics · doi:10.1093/bib/3.3.265 · Cited by 913 · cited 2×
“These regions are identified using two types of signatures: generalized profiles (weight matrices) that describe protein families and modular protein domains and patterns (regular expressions) that describe short sequence motifs often corresponding to functionally or structurally important residues (1).”
BackgroundSelf-citation
Research works printed but not linked: 13
- Sigrist, 2005, ProRule: a new database containing functional and structural information on PROSITE profiles, Bioinformatics, 21, 4060, 10.1093/bioinformatics/bti614 · DOI
- The UniProt Consortium, 2012, Reorganizing the protein space at the Universal Protein Resource (UniProt), Nucleic Acids Res., 40, D71, 10.1093/nar/gkr981 · DOI · Paper page
- de Castro, 2006, ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Res., 34, W362, 10.1093/nar/gkl124 · DOI · Paper page
- Hunter, 2012, InterPro in 2011: new developments in the family and domain prediction database, Nucleic Acids Res., 40, D306, 10.1093/nar/gkr948 · DOI · Paper page
- Sigrist, 2010, PROSITE, a protein domain database for functional characterization and annotation, Nucleic Acids Res., 38, D161, 10.1093/nar/gkp885 · DOI
- Wurm, 2011, The genome of the fire ant Solenopsis invicta, Proc. Natl Acad. Sci. USA, 108, 5679, 10.1073/pnas.1009690108 · DOI · Paper page
- Hulo, 2008, The 20 years of PROSITE, Nucleic Acids Res., 36, D245, 10.1093/nar/gkm977 · DOI · Paper page
- Levitt, 2009, Nature of the protein universe, Proc. Natl Acad. Sci. USA, 106, 11079, 10.1073/pnas.0905029106 · DOI · Paper page
- Buljan, 2009, The evolution of protein domain families, Biochem. Soc. Trans., 37, 751, 10.1042/BST0370751 · DOI
- Bastian, 2008, Bgee: integrating and comparing heterogeneous transcriptome data among species, 124, 10.1007/978-3-540-69828-9_12 · DOI
- Watschinger, 2010, Identification of the gene encoding alkylglycerol monooxygenase defines a third class of tetrahydrobiopterin-dependent enzymes, Proc. Natl Acad. Sci. USA, 107, 13672, 10.1073/pnas.1002404107 · DOI
- Watschinger, 2009, Glyceryl ether monooxygenase resembles aromatic amino acid hydroxylases in metal ion and tetrahydrobiopterin dependence, Biol. Chem., 390, 3, 10.1515/BC.2009.010 · DOI
- Soodsma, 1972, Partial characterization of the alkylglycerol cleavage enzyme system of rat liver, J. Biol. Chem., 247, 3923, 10.1016/S0021-9258(19)45123-5 · DOI
Cited by
The InterPro protein families and domains database: 20 years on
Blum, M., Chang, H.-Y., Chuguransky, S., Grego, T., Kandasaamy, S., Mitchell, A., Nuka, G., Paysan-Lafosse, T., Qureshi, M., Raj, S., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa977 · Cited by 2,231
Self-citationInterPro in 2019: improving coverage, classification and access to protein sequence annotations
Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P., Bridge, A., Brown, S. D., Chang, H.-Y., El-Gebali, S., Fraser, M. I., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1100 · Cited by 1,426
Self-citationThe Ensembl gene annotation system
Aken, B. L., Ayling, S., Barrell, D., Clarke, L., Curwen, V., Fairley, S., Fernandez Banet, J., Billis, K., García Girón, C., Hourlier, T., et al. (2016) · Database · doi:10.1093/database/baw093 · Cited by 1,086
Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN
Sievers, Q. L., Petzold, G., Bunker, R. D., Renneville, A., Słabicki, M., Liddicoat, B. J., Abdulrahman, W., Mikkelsen, T., Ebert, B. L., & Thomä, N. H. (2018) · Science · doi:10.1126/science.aat0572 · Cited by 537
“3A) highlighted shared residues that are part of the PROSITE C2H2 ZF search motif (IKZF3 C148, C151, H164, H168, and F155), residues that stabilize the ternary fold of the ZF domain (IKZF3 L161), and residues that frequently appear within C2H2 ZF domains (IKZF3 G152).”
MethodInfluentialAnnotation of biologically relevant ligands in UniProtKB using ChEBI
Coudert, E., Gehant, S., de Castro, E., Pozzato, M., Baratin, D., Neto, T., Sigrist, C. J. A., Redaschi, N., Bridge, A., The UniProt Consortium, et al. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btac793 · Cited by 350
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Metadata
- Authors
- Sigrist, C. J. A., de Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., Bougueleret, L., & Xenarios, I.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-11-17
- Volume
- 41
- Issue
- D1
- Pages
- D344-D347
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2107158607
- Cited by
- 1,562
- References
- 1
- FWCI
- 22.54
- Type
- journal article
- Language
- en
- Open access
- gold
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- Sigrist, C. J. A., de Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., Bougueleret, L., & Xenarios, I. (2012). New and continuing developments at PROSITE. Nucleic Acids Research. https://doi.org/10.1093/nar/gks1067
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