Aligning sequences to structures
McGuffin, L. J. (2008) Aligning sequences to structures. Methods in Molecular Biology, 413. pp. 61-90. ISSN 1064-3745
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Official URL: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=...
Most newly sequenced proteins are likely to adopt a similar structure to one which has already been experimentally determined. For this reason, the most successful approaches to protein structure prediction have been template-based methods. Such prediction methods attempt to identify and model the folds of unknown structures by aligning the target sequences to a set of representative template structures within a fold library. In this chapter, I discuss the development of template-based approaches to fold prediction, from the traditional techniques to the recent state-of-the-art methods. I also discuss the recent development of structural annotation databases, which contain models built by aligning the sequences from entire proteomes against known structures. Finally, I run through a practical step-by-step guide for aligning target sequences to known structures and contemplate the future direction of template-based structure prediction.