Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13

The method for protein-structure prediction, which combines the physics-based coarse-grained UNRES force field with knowledge-based modeling, has been developed further and tested in the 13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13). The method implements restraints from the consensus fragments common to server models. In this work, the server models to derive fragments have been chosen based on quality assessment, a fully automatic fragment-selection procedure has been introduced and Dynamic Fragment Assembly pseudopotentials have been fully implemented. The Global Distance Test Score (GDT_TS), averaged over our ‘Model 1’ predictions, increased by over 10 units with respect to CASP12 for the free-modeling category to reach 40.82. Our ‘Model 1’ predictions ranked 20 and 14 for all and free-modeling targets, respectively (upper 20.2% and 14.3% of all models submitted to CASP13 in these categories, respectively), compared to 27 (upper 21.1%...