title: Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 (ZECbeta) 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institut de Recerca Biomèdica and Barcelona Supercomputing Center, 10-12 08028 Barcelona, Catalonia, Spain. patrick.aloy@irbbarcelona.org
authors.forename: Patrick
authors.initials: P
authors.lastname: Aloy
authors.forename: Baldo
authors.initials: B
authors.lastname: Oliva
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D057166:High-Throughput Screening Assays; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins