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EvoDesign Logo

EvoDesign is an evolutionary profile based approach to the de novo design of proteins and protein-protein interactions. Starting from a scaffold protein (or protein complex) structure, EvoDesign first identifies protein families which have similar folds and/or interfaces from the PDB library by TM-align or iAlign, respectively. 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 simulation. The EvoDesign server includes two design options: "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 to the Service System Discussion Board and a lab member will study and answer the questions promptly ( >> more about the EvoDesign server)

Monomer Design

Copy and paste the scaffold structure (Ca-only or 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: (required)

    Protein Name: (optional)

    Interface Design

    Upload Chains Separately Upload Two-Chain Complex Structure

    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:

    Dock the two chains together: No Yes     Explanation

    Design Strategy: Redesign entire protein Redesign interface residues only     Explanation


  • 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: (required)

    Protein Name: (optional)

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

    Or you can upload the PDB file of the complex:

    Which chain should be designed: Chain 1 Chain 2


  • 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:

    Protein Name: (optional)


    Reference:

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