3DRobot is a program devoted for automated generation of diverse and well-packed protein
structure decoys. Given a native structure as input, 3DRobot first identifies diverse
structure scaffolds from a non-redundant PDB library. Restraint-free fragment reassembly
simulations are then performed to construct diverse full-length models.
The final decoys are further refined at atomic-level by a two-step iterative energy
minimization procedure to improve the hydrogen-binding networks and steric overlaps of
3DRobot aims to provide high-quality protein structural decoy sets for designing and
training protein folding force field and folding simulation methods
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Haiyou Deng, Ya Jia, Yang Zhang.
3DRobot: Automated Generation of Diverse and Well-packed Protein Structure Decoys
, Bioinformatics, in press, 2015.