FRAGPREDICT

A COMPUTER PROGRAM FOR THE PREDICTION OF PROTEASOMAL CLEAVAGE SITES AND PROTEOLYTIC FRAGMENTS

The computer program FRAGPREDICT was designed 1999 by the Institute of Biochemistry at the Medical School (Charité) of the Humboldt-University. It comprises basically two different algorithms.
One algorithms aims at predicting potential proteasomal cleavage sites (i.e. peptide bonds to be efficiently cleaved by the proteasome). It is based on a statistical analysis of cleavage-determining amino acid motifs present around the scissile bond (Holzhütter et al., 1999).
The second algorithm, which uses the results of the cleavage site analysis as an input, provides predictions of major proteolytic fragments. These predictions are based on a kinetic model of the 20S proteasome describing the time-dependent digestion of smaller (up to 40 residues long) peptide substrates (Holzhütter & Kloetzel, 2000). Owing to this length restriction of the substrates made in the model, application of the program to the prediction of proteolytic fragments derived from long protein substrates can be expected to provide reliable results only if intermediates of size 20 - 40 residues are formed which in the further course of degradation are processed in the same manner as the model substrates analysed forming the experimental basis of the model.
Both algorithms yield a probability value with which a peptide will be cleaved and a fragment will be formed, respectively. The program was trained on various data sets taken from the literature reporting on fragment patterns derived from oligomeric substrates. Cleavage of a specified peptide bond or formation of a specified fragment was termed as "observed" if the corresponding probability value was larger than 0.5. The rate of false-positive and false-negative predictions was about 10% as assessed by a jack-knife procedure (i.e. testing the predictive capacity of the model on a data set which was left out during establishment of the model).

References

Holzhütter, H.-G., Frömmel, C., and Kloetzel, P.-M. (1999).
A Theoretical Approach Towards the Identification of Cleavage-Determining Amino Acid Motifs of the 20S Proteasome. J. Mol. Biol. 286, 1251-1265
Holzhütter, H.G. and Kloetzel, P.-M. (2000).
A kinetic model of vertebrate 20S proteasome accounting for the generation of major proteolytic fragments from oligomeric peptide substrates. Biophysical J. 2000 (79): 1196-1205.