C-QUARK (stands for 'Contact-assisted QUARK') is a new method for ab initio protein structure prediction. As the name indicates, C-QUARK is extended from QUARK but significantly outperforms the latter by the integration of deep-learning based contact-map predictions into the fragment assembly simulations. C-QUARK contains three consecutive steps: First, multiple contact-maps are predicted by ResPRE and NeBcon. Second, QUARK-based replica-exchange Monte Carlo (REMC) folding simulations are performed under the guidance of a new 3-gradient contact potential. Finally, structural conformations generated in the REMC simulations are submitted to SPICKER for decoy selection, with final atomic models constructed and refined by ModRefiner and FASPR. C-QUARK participated (as 'QUARK') in the most recent community-wide CASP13 and CASP14 and was ranked one of the best server methods for ab initio (or template-free modeling, FM) structure prediction in the experiments. File format of prediction results can be found at the Help Page. For more questions, please post them at our Discussion Board.
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