Abstract
BackgroundReduced representations of proteins have been playing a keyrole in the study of protein folding. Many such models are available, with different representation detail. Although the usefulness of many such models for structural bioinformatics applications has been demonstrated in recent years, there are few intermediate resolution models endowed with an energy model capable, for instance, of detecting native or native-like structures among decoy sets. The aim of the present work is to provide a discrete empirical potential for a reduced protein model termed here PC2CA, because it employs a PseudoCovalent structure with only 2 Centers of interactions per Amino acid, suitable for protein model quality assessment.ResultsAll protein structures in the set top500H have been converted in reduced form. The distribution of pseudobonds, pseudoangle, pseudodihedrals and distances between centers of interactions have been converted into potentials of mean force. A suitable reference distribution has been defined for non-bonded interactions which takes into account excluded volume effects and protein finite size. The correlation between adjacent main chain pseudodihedrals has been converted in an additional energetic term which is able to account for cooperative effects in secondary structure elements. Local energy surface exploration is performed in order to increase the robustness of the energy function.ConclusionThe model and the energy definition proposed have been tested on all the multiple decoys' sets in the Decoys'R'us database. The energetic model is able to recognize, for almost all sets, native-like structures (RMSD less than 2.0 Å). These results and those obtained in the blind CASP7 quality assessment experiment suggest that the model compares well with scoring potentials with finer granularity and could be useful for fast exploration of conformational space. Parameters are available at the url: .
Highlights
Reduced representations of proteins have been playing a keyrole in the study of protein folding
The energetic model is able to recognize, for almost all sets, native-like structures (RMSD less than 2.0 Å). These results and those obtained in the blind CASP7 quality assessment experiment suggest that the model compares well with scoring potentials with finer granularity and could be useful for fast exploration of conformational space
For what concerns the covalent energy terms (terms i to vi in Eq (6)), only few structures, notably with short sequences, had significant deviations in the energy terms connected with the positioning of the sidechain center of mass
Summary
Reduced representations of proteins have been playing a keyrole in the study of protein folding. The potential involving a variable (e.g. a distance or an angle) is estimated from the distribution of that variable in the database, compared with that in a reference state or a null model [1,2,3,4,5,6,7,8,9,10,11] Such potentials are often referred to as statistical effective energy functions (SEEFs). This approach is strongly dependent on the methods used for building up decoys, and do not rely on an exact estimation of the energy gap existing between native and decoy structures
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