I-TASSER is an integrated package for protein structure and function predictions. For a given sequence, I-TASSER first identifies template proteins from the Protein Data Bank (PDB) by multiple threading techniques (LOMETS). The continuous fragments excised from the template alignments are used to assemble full-length models by iterative Monte Carlo simulations. The best models are then selected from the Monte Carlo trajectories by decoy clustering. The final atomic models are rebuilt from the structure clusters by atomic-level structural refinements.
An alias (runI-TASSER) is included that automatically enters the -pkgdir, -libdir, and -java_home options for you.