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EvoDesign Logo

EvoDesign is an evolutionary profile based approach to de novo protein design. Starting from a scaffold of target protein structure, EvoDesign first identifies protein families which have similar fold from the PDB library by TM-align. A structural profile is then constructed from the protein templates which is used to guide the conformation search of amino acid sequence space, where physicochemical packing is accommodated by the single-sequence based solvation, torsion angle and secondary structure predictions. The final designed sequence is obtained by clustering all sequence decoys generated during design simulations. The focus of the current server is on providing a reliable platform for sequence design with the improved fold stability and the new components with ligand-binding and interface specificities will be added in near future. Please report your questions at Service System Discussion Board and some members will study and answer the questions asap ( >> more about the EvoDesign server)

Attention: Due to a licensing issue, we can no longer use FoldX3. We have not tested the new FoldX4 force field thoroughly. You are recommended to use the default "Evolution-based only" force field whenever possible.

[Help] [Forum] [Video] [Examples]

Copy and paste scaffold structure (C-alpha only or full-atomic, in PDB format) (Click to show a sample input):

Or upload the scaffold structure file from your local computer (in PDB format):

Advanced options [?]:

  • 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

Optional information [?]: Name of your protein: Email:


Reference:
Pralay Mitra, David Shultis and Yang Zhang. EvoDesign: de novo protein design based on structural and evolutionary profiles. Nucleic Acids Res. 41: W273-W280, 2013 (Download the PDF file)

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