This page is the supportive web-site for the paper:

Searching the protein structure databank with weak sequence patterns and structural constraints

Inge Jonassen1, Ingvar Eidhammer1, Svenn H. Grindhaug1, William R. Taylor1,2

J. Mol. Biol. 304 (4), 597-617.

1Dept. of Informatics, University of Bergen, Norway
2Division of Mathematical Biology, Natl. Inst. for Medical Research, London, UK


A method is described in which proteins that match PROSITE patterns are filtered by the local root-mean-square deviation of the local 3D structures of the probe and target over the pattern components. This was found to increase the discrimination between true and false members of the protein family but was dependent on how unique the structural features in the pattern were compared to equivalent fragments extracted from structure databank. (For example; if the pattern fell in an alpha-helix, then discrimination was poor.) We then generalised the sequence patterns (by widening the range of amino acids allowed at each position) and monitored how well the structural information helped retail specificity. While the discrimination of the pure sequence pattern had generally disappeared at information content values less than 10 bits, the discrimination of the combined sequence structure probe remained high at this point before following a similar decay. The `gap' between these curves indicates that the structural component is, on average, equivalent to about 10 bits. The sequence patterns were also filtered using the structure comparison program SAP, giving a global, rather than local `view' of the proteins. This allowed the information content of the sequence patterns to become even less specific but raised problems of whether some proteins encountered with the same fold but no PROSITE pattern should constitute family members.


The links below are to two pages, the first one contains a set of Prosite families which have been analysed both using ComPat's (Prosite patterns extended with a structural probe), SAPpat (Structure Alignment guided by the Prosite patterns). The second link is to a list containing families only analysed using ComPat's. The plots are clickable; clicking on a point in a plot should give as a result a description of the corresponding pattern (and probe, if applicable). Only results from a "pure pattern" and ComPats are included in the list produced when a plot is clicked (no SAPpat results of phi-BLAST results are given).

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