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Curr Opin Struct Biol. 2006 Jun;16(3):393-8. Epub 2006 May 4.

Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction.

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  • 1Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, 1130 St Nicholas Avenue, Room 815, New York, NY 10032, USA.


The identification of geometric relationships between protein structures offers a powerful approach to predicting the structure and function of proteins. Methods to detect such relationships range from human pattern recognition to a variety of mathematical algorithms. A number of schemes for the classification of protein structure have found widespread use and these implicitly assume the organization of protein structure space into discrete categories. Recently, an alternative view has emerged in which protein fold space is seen as continuous and multidimensional. Significant relationships have been observed between proteins that belong to what have been termed different 'folds'. There has been progress in the use of these relationships in the prediction of protein structure and function.

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