Integrating Protein Secondary Structure Prediction and Multiple Sequence Alignment

Author(s): V. A. Simossis, J. Heringa.

Journal Name:Current Protein & Peptide Science

Volume 5 , Issue 4 , 2004


Modern protein secondary structure prediction methods are based on exploiting evolutionary information contained in multiple sequence alignments. Critical steps in the secondary structure prediction process are (i) the selection of a set of sequences that are homologous to a given query sequence, (ii) the choice of the multiple sequence alignment method, and (iii) the choice of the secondary structure prediction method. Because of the close relationship between these three steps and their critical influence on the prediction results, secondary structure prediction has received increased attention from the bioinformatics community over the last few years. In this treatise, we discuss recent developments in computational methods for protein secondary structure prediction and multiple sequence alignment, focus on the integration of these methods, and provide some recommendations for state-of-the-art secondary structure prediction in practice.

Keywords: sequence database searching, secondary structure prediction, multiple sequence alignment

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Article Details

Year: 2004
Page: [249 - 266]
Pages: 18
DOI: 10.2174/1389203043379675
Price: $58