UCL logo

UCL Discovery

UCL home » Library Services » Electronic resources » UCL Discovery

Benchmarking secondary structure prediction for fold recognition

McGuffin, LJ; Jones, DT; (2003) Benchmarking secondary structure prediction for fold recognition. PROTEINS , 52 (2) 166 - 175. 10.1002/prot.10408.

Full text not available from this repository.

Abstract

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. (C) 2003 Wiley-Liss, Inc.

Type:Article
Title:Benchmarking secondary structure prediction for fold recognition
DOI:10.1002/prot.10408
Keywords:protein structure prediction, secondary structure element alignment, segment overlap score, Q(3) score, prediction errors, PROTEIN-STRUCTURE, CLASSIFICATION, SEQUENCE, SERVERS
UCL classification:UCL > School of BEAMS > Faculty of Engineering Science > Computer Science

Archive Staff Only: edit this record