Benchmarking secondary structure prediction for fold recognition

McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 and Jones, D. T. (2003) Benchmarking secondary structure prediction for fold recognition. Proteins: Structure, Function, and Genetics, 52 (2). pp. 166-175. ISSN 0887-3585 doi: 10.1002/prot.10408

Abstract/Summary

If secondary structure predictions are to be incorporated into fold recognition methods, an assessment of the effect of specific types of errors in predicted secondary structures on the sensitivity of fold recognition should be carried out. Here, we present a systematic comparison of different secondary structure prediction methods by measuring frequencies of specific types of error. We carry out an evaluation of the effect of specific types of error on secondary structure element alignment (SSEA), a baseline fold recognition method. The results of this evaluation indicate that missing out whole helix or strand elements, or predicting the wrong type of element, is more detrimental than predicting the wrong lengths of elements or overpredicting helix or strand. We also suggest that SSEA scoring is an effective method for assessing accuracy of secondary structure prediction and perhaps may also provide a more appropriate assessment of the “usefulness” and quality of predicted secondary structure, if secondary structure alignments are to be used in fold recognition.

Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/27437
Item Type	Article
Refereed	Yes
Divisions	Life Sciences > School of Biological Sciences > Biomedical Sciences No Reading authors. Back catalogue items
Publisher	Wiley
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