Most successful structure prediction 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 predictions 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 prediction servers.

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Persistent URL dx.doi.org/10.1016/j.cplett.2014.07.014
Journal Chemical Physics Letters
Citation
Ruiz-Blanco, Y.B. (Yasser B.), Marrero-Ponce, Y. (Yovani), García, Y. (Yamila), Puris, A. (Amilkar), Bello, R. (Rafael), Green, J, & Sotomayor-Torres, C.M. (Clivia M.). (2014). A physics-based scoring function for protein structural decoys: Dynamic testing on targets of CASP-ROLL. Chemical Physics Letters, 610-611, 135–140. doi:10.1016/j.cplett.2014.07.014