This website contains two sets of I-TASSER structural decoys for 56 non-homologous single-domain proteins. Please address questions to: yangzhanglabumich.edu.

• The Decoy Set I was taken from the trajectories of the I-TASSER simulations which include 12,500-32,000 raw decoys for each protein target. The backbone structure is built by I-TASSER ab initio simulation and the side-chain atoms are added using Pulchra. This decoy set was used to test the SPICKER clutering program for identifying best near-native structures. Please refer to the following paper for detail of the Decoy Set I: S Wu, J Skolnick, Y Zhang: Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biology 2007, 5: 17.
  

• The Decoy Set II is a structurally non-redundant set of protein structures which were selected from the Decoy Set I. Each protein target contains 300-500 decoys. Each decoy structure was first generated by I-TASSER Monte Carlo simulations and then refined by GROMACS4.0 MD simulation using OPLS-AA force field with the purpose of removing steric clashes and improving hydrogen-bonding network. This decoy set was used to test the ability of atomic potentials, including RW and RWplus potentials, for near-native structure identification and RMSD-energy correlation. Please refer to the following paper for detail of Decoy Set II: J Zhang and Y Zhang, A Distance-Dependent Atomic Potential Derived from Random-Walk Ideal Chain Reference State for Protein Fold Selection and Structure Prediction. PLoS One, vol 5, e15386 (2010).