PROSITE

PROSITE: a documented database using patterns and profiles as motif. Among the various databases dedicated to the identification of protein families and domains, PROSITE is the first one created and has continuously evolved since. PROSITE currently consists of a large collection of biologically meaningful motifs that are described as patterns or profiles, and linked to documentation briefly describing the protein family or domain they are designed to detect. The close relationship of PROSITE with the SWISS-PROT protein database allows the evaluation of the sensitivity and specificity of the PROSITE motifs and their periodic reviewing. In return, PROSITE is used to help annotate SWISS-PROT entries. The main characteristics and the techniques of family and domain identification used by PROSITE are reviewed in this paper. descriptors


References in zbMATH (referenced in 23 articles )

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  1. Carmel, Amir; Tsur, Dekel; Ziv-Ukelson, Michal: On almost Monge all scores matrices (2019)
  2. Axelson-Fisk, Marina: Comparative gene finding. Models, algorithms and implementation (2015)
  3. Chen, Yen-Kuang; Li, Kuo-Bin: Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou’s pseudo amino acid composition (2013)
  4. Marschall, Tobias: Construction of minimal deterministic finite automata from biological motifs (2011)
  5. Wong, Ka-Chun; Peng, Chengbin; Wong, Man-Hon; Leung, Kwong-Sak: Generalizing and learning protein-DNA binding sequence representations by an evolutionary algorithm (2011) ioport
  6. Rahbar, Mohammad Reza; Rasooli, Iraj; Mousavi Gargari, Seyed Latif; Amani, Jafar; Fattahian, Yaser: In silico analysis of antibody triggering biofilm associated protein in \textitAcinetobacterbaumannii (2010)
  7. Sigrist, Christian J. A.; Cerutti, Lorenzo; De Castro, Edouard; Langendijk-Genevaux, Petra S.; Bulliard, Virginie; Bairoch, Amos; Hulo, Nicolas: PROSITE, a protein domain database for functional characterization and annotation (2010) ioport
  8. Rendon, Gloria; Ger, Mao-Feng; Kantorovitz, Ruth; Natarajan, Shreedhar; Tilson, Jeffrey; Jakobsson, Eric: Understanding the “horizontal dimension” of molecular evolution to annotate, classify, and discover proteins with functional domains (2009) ioport
  9. Xu, Ying: Computational challenges in deciphering genomic structures of bacteria (2009) ioport
  10. Dogruel, Mutlu; Down, Thomas A.; Hubbard, Tim J. P.: Nestedmica as an ab initio protein motif discovery tool (2008) ioport
  11. Hernandez, David; Gras, Robin; Appel, Ron: Neighborhood functions and hill-climbing strategies dedicated to the generalized ungapped local multiple alignment (2008)
  12. Hulo, Nicolas; Bairoch, Amos; Bulliard, Virginie; Cerutti, Lorenzo; Cuche, Béatrice A.; De Castro, Edouard; Lachaize, Corinne; Langendijk-Genevaux, Petra S.; Sigrist, Christian J. A.: The 20 years of PROSITE. (2008) ioport
  13. Ng, Yen Kaow; Shinohara, Takeshi: Developments from enquiries into the learnability of the pattern languages from positive data (2008)
  14. Chung, Yun-Sheng; Lu, Chin Lung; Tang, Chuan Yi: Efficient algorithms for regular expression constrained sequence alignment (2007)
  15. Livesay, Dennis R.; Kidd, Patrick D.; Eskandari, Sepehr; Roshan, Usman: Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na^+ symporter family (2007) ioport
  16. Mistry, Jaina; Bateman, Alex; Finn, Robert D.: Predicting active site residue annotations in the pfam database (2007) ioport
  17. Nebel, Jean-Christophe; Herzyk, Pawel; Gilbert, David R.: Automatic generation of 3D motifs for classification of protein binding sites (2007) ioport
  18. Tobi, Dror; Bahar, Ivet: Recruitment of rare 3-grams at functional sites: Is this a mechanism for increasing enzyme specificity? (2007) ioport
  19. Yu, Huan; Qian, Minping; Deng, Minghua: Understanding protein-protein interactions: from domain level to motif level (2007)
  20. Hulo, Nicolas; Bairoch, Amos; Bulliard, Virginie; Cerutti, Lorenzo; De Castro, Edouard; Langendijk-Genevaux, Petra S.; Pagni, Marco; Sigrist, Christian J. A.: The PROSITE database. (2006) ioport

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