FoldDesign is a fragment-assembly based approach to de novo protein scaffold design.
Starting from user-defined constraints (secondary structure and/or contact and distance maps),
FoldDesign first identifies a set of 1-20 residue fragments from the PDB that match the desired
secondary structure.
Course-grained structural decoys with desired folds satisfying the constraints
are then constructed by replica-exchange Monte Carlo simulations under the guidance
of a sequence-independent generic force field.
Next, the generated structure decoys are clustered with the lowest energy model from
the largest cluster selected.
Finally, atomic-level structural refinement and sequence design are carried out
iteratively on the selected designs with both structural scaffold and
designed sequence returned in the output.
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