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A physics-based scoring function for protein structural decoys: Dynamic testing on targets of CASP-ROLL

Abstract:

Most successful structure pbkp_rediction strategies use knowledge-based functions for global optimization, in spite of their intrinsic limited potential to create new folds, while physics-based approaches are often employed only during structure refinement steps. We here propose a physics-based scoring potential intended to perform global searches of the conformational space. We introduce a dynamic test to evaluate the discrimination power of our function, and compare it with pbkp_redictions of targets from the CASP-ROLL competition. Results demonstrate that this dynamic test is able to generate 3D models which outrank 59% (according GDT-TS score) of models generated with ab initio structure pbkp_rediction servers. © 2014 Elsevier B.V.