Check out software developed by our group and other open-source freebies at ISB Lab GitHub.
Many of the packages we develop are integrated with the Integrative modeling Platform IMP, which we use to model protein assemblies.
PrISM : Package to annotate high- and low-precision regions in integrative structure models. Works on models from IMP as well as integrative models produced by other software [in PDB format]. Now used by wwPDB to validate integrative models!
Scoring functions: PISA (atomic), PIE (residue), and C3 (combination) scoring functions for ranking models of protein-protein complexes produced by docking programs.
Other utilities: Contains scripts for calculating interface RMSD, and other utilities for modifying PDBs, adding chain names, running Modeller etc.