Journal of Molecular Biology
CommunicationProtein secondary structure prediction based on position-specific scoring matrices1
Section snippets
Method
The prediction method (illustrated in Figure 1) is split into three stages: generation of a sequence profile, prediction of initial secondary structure, and finally the filtering of the predicted structure.
Results
Figure 2(a) and (b) shows the distributions of Q3 scores and Sov3 scores (Rost et al., 1994) for the testing set of 187 protein chains. Note that the average Q3 score for these 187 proteins, calculated by chain, is found to be 76.0 % with a standard deviation of 7.8 %. The average Sov3 score was 73.5 % with a standard deviation of 12.7 %. Taken by residue (i.e. averaging with weighting by sequence length), the average Q3 score is 76.5 %. Using the simpler DSSP mapping, which results in a higher
Conclusions
At this stage it is not yet clear which factors contribute most to the success of the PSIPRED method, and work is currently underway to compare the results obtained from PSIPRED with those obtained from other methods, but using the same input profiles. There are three aspects of the PSI-BLAST program that no doubt contribute, perhaps equally, to the success of PSIPRED. Firstly the alignments produced by PSI-BLAST are based on pairwise local alignments. Previous work Frishman and Argos 1997,
Availability
The PSIPRED Web server, along with the software and test sets used here may be obtained electronically from the following address: http://globin.bio.warwick.ac.uk/psipred. Benner & Gerloff (1990)
Acknowledgements
This work was supported by The Royal Society.
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