●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

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.

Cut and paste your sequence (in FASTA format, less than 500 residues. Example input


Or upload sequence from your computer:

Email: (mandatory, where results will be sent to.)


ID: (optional, name of the protein)


Advanced options [?]

• Assign contact map: Example contact [?] (Residue index starts from 1)
  

  Or upload sequence from your computer:
  
  

• Exclude fragments: [?]
  keep all identified fragments (recommended)
  remove fragments from protein sharing >30% sequence identity with target
  

• Download the C-QUARK standalone package and libraries
• Download the C-QUARK benchmark dataset

References:

• S. M. Mortuz, Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Yang Zhang. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications, 12: 5011 (2021). [PDF] [Support Information]