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Input parameters:

Contact map file:       
FASTA file:
Contact cutoff:
Run number:
Exemplary contact map file (.cmap) and FASTA file (.fasta) can be downloaded here.


The C2Sv2.0 service allows to reconstruct full-atom protein structures based on contact maps. The needed inputs are the protein sequence in a FASTA file (FASTA example) and the contact map in a matrix format (CMAP example).


C2Sv2.0 is a three-step procedure which uses available bioinformatic applications. First, the 3D coordinates of C-alpha atoms are estimated based on constraints imposed by the contact map (FT-COMAR) (Vassura et al., 2008). This is followed by the backbone reconstruction (REMO) (Li and Zhang) and side-chain modeling (SCWRL) (Krivov et al., 2009).

How to cite

If you used our pipeline please cite our work and all the tools that are embedded in the procedure:

Konopka BM, Ciombor M, Kurczynska M, Kotulska M, Automated procedure for contact-map-based protein structure reconstruction, J Membr Biol, 2014 May;247(5):409-20.
Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R, FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps, Bioinformatics, 2008 May 15;24(10):1313-5.
Yunqi Li and Yang Zhang, REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks, Proteins, 2009, 76: 665-676.
Krivov GG, Shapovalov MV, Dunbrack RL Jr, Improved prediction of protein side-chain conformations with SCWRL4, Proteins, 2009 Dec;77(4):778-95.


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