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.
zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417