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. Please report your questions to the Service System Discussion Board.

Submit Job

• Sequence
• File

Input the desired 3-state secondary structure (H=helix, E=strand,C=coil) with length between [20,1500] residues

Input the desired 3-state secondary structure (H=helix, E=strand,C=coil) with length between [20,1500] residues

Optional Input: Add user-defined contact/distance restraints

Email

Protein Name (optional)

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Reference

• Robin Pearce, Xiaoqiang Huang, Gilbert S. Omenn, Yang Zhang. De Novo Protein Fold Design by Assembling Structural Fragments Under the Guidance of an Optimized Force Field, submitted, 2022