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EvoDesign Logo

EvoDesign is an evolutionary profile based approach to de novo design of proteins and protein-protein interactions. Starting from a scaffold of target protein (or protein complex) structure, EvoDesign first identifies protein families which have similar folds and/or interfaces from the PDB library by TM-align. Multiple structural profiles are then constructed from the protein and protein-interface templates, which are used to guide the search of amino acid sequence space, where physicochemical side-chain and backbone packing is accommodated by a newly constructed physics- and knowledge-based force field. The final designed sequences are selected through clustering all sequence decoys generated during the Monte Carlo design simulations. The EvoDesign server includes two interfaces of "Monomer Design" and "Interface Design", which take monomer and complex structures and are designed for protein fold and protein-protein interaction designs, respectively. Please report your questions at Service System Discussion Board and some members will study and answer the questions asap ( >> more about the EvoDesign server)

Monomer Design

Copy and paste the scaffold structure (full-atomic) in PDB format
(Click to show a sample input):

Or you can upload the PDB scaffold file:


  • Fold cutoff: TM-score >    Explanation
  • Force field: Evolution-based only Evolution and Physics-based
  • Residue restrictions:
    • excluding residue types   (e.g. D:16 G:23)   Explanation
    • freezing some residues   (e.g. 16, 33, 51)   Explanation

  • Model structure of designed sequences using I-TASSER:       No Yes     Explanation


  • E-mail: (optional)

    Protein Name: (optional)

    Interface Design

    Copy and paste the structure of the protein you want to design (full-atomic) in PDB format
    (Click to show a sample input):

    Or you can upload the PDB file of the protein you want to design:

    Copy and paste the structure of the protein that your scaffold binds to (full-atomic) in PDB format
    (Click to show a sample input):

    Or you can upload the PDB file of the protein that your scaffold binds to:


  • Fold cutoff: TM-score >    Explanation
  • Residue restrictions:
    • excluding residue types   (e.g. D:16 G:23)   Explanation
    • freezing some residues   (e.g. 16, 33, 51)   Explanation

  • Model structure of designed sequences using I-TASSER:       No Yes     Explanation


  • E-mail: (optional)

    Protein Name: (optional)


    Reference:

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