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Open Access Highly Accessed Methodology article

Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations

Patrick Aloy12 and Baldo Oliva3*

Author Affiliations

1 Institut de Recerca Biomèdica (IRB) and Barcelona Supercomputing Center (BSC), c/Baldiri i Reixac, 10-12 08028 Barcelona, Catalonia, Spain

2 Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23 08010-Barcelona, Catalonia, Spain

3 Structural Bioinformatics Group, (GRIB-IMIM), Departament de Ciències Eperimentals i de la Salut, Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB), 08003-Barcelona, Catalonia, Spain

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BMC Structural Biology 2009, 9:71  doi:10.1186/1472-6807-9-71

Published: 16 November 2009



Recent advances on high-throughput technologies have produced a vast amount of protein sequences, while the number of high-resolution structures has seen a limited increase. This has impelled the production of many strategies to built protein structures from its sequence, generating a considerable amount of alternative models. The selection of the closest model to the native conformation has thus become crucial for structure prediction. Several methods have been developed to score protein models by energies, knowledge-based potentials and combination of both.


Here, we present and demonstrate a theory to split the knowledge-based potentials in scoring terms biologically meaningful and to combine them in new scores to predict near-native structures. Our strategy allows circumventing the problem of defining the reference state. In this approach we give the proof for a simple and linear application that can be further improved by optimizing the combination of Zscores. Using the simplest composite score () we obtained predictions similar to state-of-the-art methods. Besides, our approach has the advantage of identifying the most relevant terms involved in the stability of the protein structure. Finally, we also use the composite Zscores to assess the conformation of models and to detect local errors.


We have introduced a method to split knowledge-based potentials and to solve the problem of defining a reference state. The new scores have detected near-native structures as accurately as state-of-art methods and have been successful to identify wrongly modeled regions of many near-native conformations.