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Curr Opin Struct Biol. 2015 Jun;32:33-8. doi: 10.1016/j.sbi.2015.01.007. Epub 2015 Feb 10.

Template-based prediction of protein function.

Author information

1
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Department of Systems Biology, Center for Computational Biology and Bioinformatics, 1130 St. Nicholas Avenue, Room 815, New York, NY 10032, United States. Electronic address: dsp18@columbia.edu.
2
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Department of Systems Biology, Center for Computational Biology and Bioinformatics, 1130 St. Nicholas Avenue, Room 815, New York, NY 10032, United States.

Abstract

We discuss recent approaches for structure-based protein function annotation. We focus on template-based methods where the function of a query protein is deduced from that of a template for which both the structure and function are known. We describe the different ways of identifying a template. These are typically based on sequence analysis but new methods based on purely structural similarity are also being developed that allow function annotation based on structural relationships that cannot be recognized by sequence. The growing number of available structures of known function, improved homology modeling techniques and new developments in the use of structure allow template-based methods to be applied on a proteome-wide scale and in many different biological contexts. This progress significantly expands the range of applicability of structural information in function annotation to a level that previously was only achievable by sequence comparison.

PMID:
25678152
PMCID:
PMC4512936
DOI:
10.1016/j.sbi.2015.01.007
[Indexed for MEDLINE]
Free PMC Article

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