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 the structures. 3DRobot aims to provide high-quality protein structural decoy sets for designing and training protein folding force field and folding simulation methods.
The 3DRobot webserver is available at: https://zhanglab.ccmb.med.umich.edu/3DRobot.
- Download 3DRobot standalone program: 3DRobot1.0.tar.bz2 (27MB)
- Download non-redundant PDB library: PDBlib.tar.bz2 (540MB)
- Download 3DRobot pre-generated structure decoys: 3DRobot Decoy Sets
- Haiyou Deng, Ya Jia*, Yang Zhang*. 3DRobot: Automated Generation of Diverse and Well-packed Protein Structure Decoys. Boinformatics, 32: 378-87 (2016).