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.
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Nucleic Acids Res. 2013 Jul;41(Web Server issue):W273-80. doi: 10.1093/nar/gkt384. Epub 2013 May 13.
EvoDesign: De novo protein design based on structural and evolutionary profiles.
Mitra P, Shultis D, Zhang Y.