The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
You may want to look also at CS-Rosetta.
Freely available to academic users (see #Licence). If you won't apply for the licence, following modules will not work for you. Modules:
rosetta-3.8 rosetta-3.7 rosetta-2.3
Initialize environment with command:
module add rosetta-3.8
Notice: This application supports parallel computing (MPI, OpenMP) which can have weird consequences. For more details about parallel computing visit the page How to compute/Parallelization.
Documentation is at https://www.rosettacommons.org/docs/latest/Home .