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QUARK is a computer algorithm for ab initio protein structure prediction and protein peptide folding, which aims to construct the correct protein 3D model from amino acid sequence only. QUARK models are built from small fragments (1-20 residues long) by replica-exchange Monte Carlo simulation under the guide of an atomic-level knowledge-based force field. QUARK was ranked as the No 1 server in Free-modeling (FM) in CASP9 and CASP10 experiments. Since no global template information is used in QUARK simulation, the server is suitable for proteins that do not have homologous templates in the PDB library. Go to example to view an example of QUARK output. The server is only for non-commercial use. Questions about the QUARK server can be posted at the Service System Discussion Board.

Cut and paste your sequence (in FASTA format, less than 200 AA. Example input

Or upload sequence from your computer:

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

Password: (mandatory, click here if you do not have a QUARK password)

ID: (optional, name of the protein)


Advanced options [?]

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

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QUARK Resource:

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Reference:

• D Xu and Y Zhang. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins, 2012, 80, 1715-1735 (2012). [PDF] [Support Information].
• SM Mortuz, W Zheng, C Zhang, Y Li, R Pearce, Y Zhang. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications, 12: 5011 (2021). [PDF] [Support Information].