A tool to aid in prediction of sites of limited proteolysis

The prediction program, NICKPRED, has been made available via the internet and can be reached via the URL: http://sjh.bi.umist.ac.uk/nickpred.html (Figure 3). Users may obtain predictions from structures in the current release of the Brookhaven Databank (27) or may submit their own models/structures in PDB format. Results are returned via e-mail. The output options of the software allow the user access to the raw, normalized conformational parameter scores, as well as the processed prediction scores on a residue-by-residue basis and collated statistics on putative and non-putative nicksites. Furthermore, a simple Rasmol output script can be sent via e-mail which may be saved and quickly run which colours the structure by prediction score (from 0 to 1, 1 being the most highly predicted). A sample prediction profile for the protein elastase is shown in Figure 4, along with the Rasmol image showing the prediction score along the protein backbone (Figure 5).

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Figure 3 The MICKPRED Web server submission page. Users may enter a Brook haven four-letter code identifier or upload one of their own PDB format files from their local computer. Users may control which proteinase is to be considered as a cleavage agent, as well as the conformational parameters to use as predictors. The optimized weights and windows are used as defaults. Varying output formats may be specified, which are returned via electronic mail to the user.

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