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Open Access Highly Accessed Open Badges Research article

Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins

Ranjit Prasad Bahadur12 and Pinak Chakrabarti1*

Author Affiliations

1 Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India

2 Current address: Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, West Bengal, India

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BMC Structural Biology 2009, 9:76  doi:10.1186/1472-6807-9-76

Published: 28 December 2009



Setting the rules for the identification of a stable conformation of a protein is of utmost importance for the efficient generation of structures in computer simulation. For structure prediction, a considerable number of possible models are generated from which the best model has to be selected.


Two scoring functions, Rs and Rp, based on the consideration of packing of residues, which indicate if the conformation of an amino acid sequence is native-like, are presented. These are defined using the solvent accessible surface area (ASA) and the partner number (PN) (other residues that are within 4.5 Å) of a particular residue. The two functions evaluate the deviation from the average packing properties (ASA or PN) of all residues in a polypeptide chain corresponding to a model of its three-dimensional structure. While simple in concept and computationally less intensive, both the functions are at least as efficient as any other energy functions in discriminating the native structure from decoys in a large number of standard decoy sets, as well as on models submitted for the targets of CASP7. Rs appears to be slightly more effective than Rp, as determined by the number of times the native structure possesses the minimum value for the function and its separation from the average value for the decoys.


Two parameters, Rs and Rp, are discussed that can very efficiently recognize the native fold for a sequence from an ensemble of decoy structures. Unlike many other algorithms that rely on the use of composite scoring function, these are based on a single parameter, viz., the accessible surface area (or the number of residues in contact), but still able to capture the essential attribute of the native fold.