OBJECTIVE: Protein structure prediction (PSP) aims to reconstruct the 3D structure of a given protein starting from its primary structure (chain of amino acidic residues). It is a well-known fact that the 3D structure of a protein only depends on its primary structure. PSP is one of the most important and still unsolved problems in computational biology. Protein structure selection (PSS), instead of reconstructing a 3D model for the given chain, aims to select among a given, possibly large, number of 3D structures (called decoys) those that are closer (according to a given notion of distance) to the original (unknown) one. In this paper we address PSS problem using graph theoretic techniques. METHODS AND MATERIALS: Existing methods for solving PSS make use of suitably defined energy functions which heavily rely on the primary structure of the protein and on protein chemistry. In this paper we present a new approach to PSS which does not take advantage of the knowledge of the primary structure of the protein but only depends on the graph theoretic properties of the decoys graphs (vertices represent residues and edges represent pairs of residues whose Euclidean distance is less than or equal to a fixed threshold). RESULTS: Even if our methods only rely on approximate geometric information, experimental results show that some of the adopted graph properties score similarly to energy-based filtering functions in selecting the best decoys. CONCLUSION: Our results highlight the principal role of geometric information in PSS, setting a new starting point and filtering method for existing energy function-based techniques.
A graph theoretic approach to protein structure selection
Fariselli, Piero;
2009-01-01
Abstract
OBJECTIVE: Protein structure prediction (PSP) aims to reconstruct the 3D structure of a given protein starting from its primary structure (chain of amino acidic residues). It is a well-known fact that the 3D structure of a protein only depends on its primary structure. PSP is one of the most important and still unsolved problems in computational biology. Protein structure selection (PSS), instead of reconstructing a 3D model for the given chain, aims to select among a given, possibly large, number of 3D structures (called decoys) those that are closer (according to a given notion of distance) to the original (unknown) one. In this paper we address PSS problem using graph theoretic techniques. METHODS AND MATERIALS: Existing methods for solving PSS make use of suitably defined energy functions which heavily rely on the primary structure of the protein and on protein chemistry. In this paper we present a new approach to PSS which does not take advantage of the knowledge of the primary structure of the protein but only depends on the graph theoretic properties of the decoys graphs (vertices represent residues and edges represent pairs of residues whose Euclidean distance is less than or equal to a fixed threshold). RESULTS: Even if our methods only rely on approximate geometric information, experimental results show that some of the adopted graph properties score similarly to energy-based filtering functions in selecting the best decoys. CONCLUSION: Our results highlight the principal role of geometric information in PSS, setting a new starting point and filtering method for existing energy function-based techniques.
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