12833541

Source:http://linkedlifedata.com/resource/pubmed/id/12833541

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0162807, umls-concept:C0332462, umls-concept:C0524637, umls-concept:C0525063, umls-concept:C0681842
pubmed:issue	2
pubmed:dateCreated	2003-6-30
pubmed:abstractText	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.
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/8700181
pubmed:citationSubset	IM
pubmed:chemical	http://linkedlifedata.com/resource/pubmed/chemical/Proteins
pubmed:status	MEDLINE
pubmed:month	Aug
pubmed:issn	1097-0134
pubmed:author	pubmed-author:JonesDavid TDT, pubmed-author:McGuffinLiam JLJ
pubmed:copyrightInfo	Copyright 2003 Wiley-Liss, Inc.
pubmed:issnType	Electronic
pubmed:day	1
pubmed:volume	52
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	166-75
pubmed:dateRevised	2006-11-15
pubmed:meshHeading	pubmed-meshheading:12833541-Models, Molecular, pubmed-meshheading:12833541-Protein Folding, pubmed-meshheading:12833541-Protein Structure, Secondary, pubmed-meshheading:12833541-Proteins, pubmed-meshheading:12833541-Reproducibility of Results
pubmed:year	2003
pubmed:articleTitle	Benchmarking secondary structure prediction for fold recognition.
pubmed:affiliation	Bioinformatics Unit, Department of Computer Science, University College London, London, United Kingdom. l.mcguffin@cs.ucl.ac.uk
pubmed:publicationType	Journal Article, Comparative Study, Research Support, Non-U.S. Gov't, Evaluation Studies