The PROSITE database
Nicolas Hulo,Amos Marc Bairoch,Virginie Bulliard,Lorenzo Cerutti,Edouard de Castro,Petra S. Langendijk-Genevaux,Marco Pagni,Christian J. A. Sigrist +7 more
TL;DR: The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles that provides useful biological information on the protein family, domain or functional site identified by the signature.
read more
Abstract: The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to a documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE database is now complemented by a series of rules that can give more precise information about specific residues. During the last 2 years, the documentation and the ScanProsite web pages were redesigned to add more functionalities. The latest version of PROSITE (release 19.11 of September 27, 2005) contains 1329 patterns and 552 profile entries. Over the past 2 years more than 200 domains have been added, and now 52% of UniProtKB/Swiss-Prot entries (release 48.1 of September 27, 2005) have a cross-reference to a PROSITE entry. The database is accessible at http://www.expasy.org/prosite/.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Comparative protein structure modeling using Modeller.
Narayanan Eswar,Ben Webb,Marc A. Marti-Renom,Mallur S. Madhusudhan,David Eramian,Min-Yi Shen,Ursula Pieper,Andrej Sali +7 more
TL;DR: This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
Comparative Protein Structure Modeling Using MODELLER
Narayanan Eswar,Ben Webb,Marc A. Marti-Renom,Mallur S. Madhusudhan,David Eramian,Min-Yi Shen,Ursula Pieper,Andrej Sali +7 more
TL;DR: This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications.
InterPro: the integrative protein signature database
Sarah Hunter,Rolf Apweiler,Teresa K. Attwood,Amos Marc Bairoch,Alex Bateman,David Binns,Peer Bork,Ujjwal Das,Louise C. Daugherty,Lauranne Duquenne,Robert D. Finn,Julian Gough,Daniel H. Haft,Nicolas Hulo,Daniel Kahn,Elizabeth Kelly,Aurélie Laugraud,Ivica Letunic,David M. Lonsdale,Rodrigo Lopez,Martin Madera,John Maslen,Craig McAnulla,Jennifer McDowall,Jaina Mistry,Alex L. Mitchell,Nicola Mulder,Darren A. Natale,Christine A. Orengo,Antony F. Quinn,Jeremy D. Selengut,Christian J. A. Sigrist,Manjula Thimma,Paul Thomas,Franck Valentin,Derek Wilson,Cathy H. Wu,Corin Yeats +37 more
TL;DR: The InterPro database integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs.
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
Edouard de Castro,Christian J. A. Sigrist,Alexandre Gattiker,Virginie Bulliard,Petra S. Langendijk-Genevaux,Elisabeth Gasteiger,Amos Marc Bairoch,Nicolas Hulo +7 more
TL;DR: A new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences that makes use of ProRules—context-dependent annotation templates—to detect functional and structural intra-domain residues.
1.7K
References
Mechanisms and functions of eph and ephrin signalling
Klas Kullander,Rüdiger Klein +1 more
TL;DR: The concept of bidirectional signalling has emerged as an important mechanism by which Ephs and ephrins control the output signal in processes of cell–cell communication.
1.2K
PROSITE: A documented database using patterns and profiles as motif descriptors
Christian J. A. Sigrist,Lorenzo Cerutti,Nicolas Hulo,Alexandre Gattiker,Laurent Falquet,Marco Pagni,Amos Marc Bairoch,Philipp Bucher +7 more
TL;DR: 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.
•Book
Markov models
Michael Kuperberg
- 01 Jan 2008
TL;DR: In this paper, the authors define stochastic processes as a sequence of non-i.i.d. random variables, and define the joint density using the chain rule.
170
MSDsite: A database search and retrieval system for the analysis and viewing of bound ligands and active sites
TL;DR: The three‐dimensional environments of ligand binding sites have been derived from the parsing and loading of the PDB entries into a relational database and a fast interactive search and retrieval system has been developed.
106
Expression of a kinase-defective Eph-like receptor in the normal human brain.
Hiroshi Matsuoka,Nobuko Iwata,Mitsuhiro Ito,Manabu Shimoyama,Aki Nagata,Kazuo Chihara,Setsuo Takai,Toshimitsu Matsui +7 more
TL;DR: HEP is the first description of a kinase-defective Eph-family protein expressed abundantly in normal human tissues and was expressed in the human brain as much as in CHO-K1 cells transfected with a HEP cDNA expression vector.
60
Related Papers (5)
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more