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J Biomol Struct Dyn. 2004 Jun;21(6):725-36.

Protein decoy sets for evaluating energy functions.

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  • 1Center of Applied Molecular Engineering, Institute of Chemistry and Biochemistry, University of Salzburg, Jakob Haringerstrabe 3, A-5020 Salzburg, Austria. dgilis@ulb.ac.be

Abstract

Energy functions are crucial ingredients of protein tertiary structure prediction methods. Assessing the quality of energy functions is therefore of prime importance. It requires the elaboration of a standard evaluation scheme, whose key elements are: i). sets that contain the native and several non-native structures of proteins (decoys) in order to test whether the energy functions display the expected quality features and ii). measures to evaluate the reliability of energy functions. We present here a survey of the recent advances in these two related fields. In a first part, we analyze and review the large number of decoy sets that are available on the web, and we summarize the characteristics of a challenging decoy set. We then discuss how to define the quality of energy functions and review the measures related to it.

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