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.2004 Jan 1;32(Database issue):D134-7.
doi: 10.1093/nar/gkh044.

Recent improvements to the PROSITE database

Affiliations

Recent improvements to the PROSITE database

Nicolas Hulo et al. Nucleic Acids Res..

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 documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements. We also introduced the facility to search PDB with a PROSITE entry or a user's pattern and visualize matched positions on 3D structures. The latest version of PROSITE (release 18.17 of November 30, 2003) contains 1676 entries. The database is accessible at http://www.expasy.org/prosite/.

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Figures

Figure 1
Figure 1
A search on the PDB database with the PROSITE pattern PS00107 (directed against the ATP binding region of the kinase domain) was performed on the ScanProsite page. The pattern identified 221 matches. The 1CTP entry was selected to visualize the position of the pattern on the 3D structure. The ATP binding region is highlighted in red. The ScanProsite page uses RasMol (16) scripts to produce images. An interactive view with the Chime program is also provided.
Figure 2
Figure 2
Five proteins have been extracted from the domain view of the trypsin profile (PS50240) match list. Disulfide bridges are represented as red inverted hooks and active sites as red diamonds. The labeling of the active site residues allows the rapid detection of domains that may have lost their enzymatic activity. The fifth example is the human haptoglobin, a clearly related serine protease but with no enzymatic activity.
See this image and copyright information in PMC

References

    1. Sigrist C.J.A., Cerutti,L., Hulo,N., Gattiker,A., Falquet,L., Pagni,M., Bairoch,A. and Bucher,P. (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief. Bioinform., 3, 265–274. - PubMed
    1. Gribskov M., Luthy,R. and Eisenberg,D. (1990) Profile analysis. Methods Enzymol., 183, 146–159. - PubMed
    1. Bucher P., Karplus,K., Moeri,N. and Hofmann,K. (1996) A flexible motif search technique based on generalized profiles. Comput. Chem., 20, 3–23. - PubMed
    1. Hofmann K. (2000) Sensitive protein comparisons with profiles and hidden Markov models. Brief. Bioinform., 1, 167–178. - PubMed
    1. Pagni M. and Jongeneel,C.V. (2001) Making sense of score statistics for sequence alignments. Brief. Bioinform., 2, 51–67. - PubMed

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