Constrained NMA for loop modeling

Stability prediction upon mutation

Orientational coarse-grained potential for protein & loop modeling

Efficient loop closure engine for protein loop prediction (rcd.chaconlab.org) 

Flexible fitting of atomic structures into EM maps

Effective coarse-grained knowledge-based scoring function for protein-ligand interactions

Structural prediction of protein-protein interactions

Normal Mode Analysis in internal coordinates

Ab initio 3D modeling of solution scattering profiles

Package for the modeling and refinement of multi-scale biomolecular EM structures (external Wriggers' lab)

Ultra-fast multiresolution rigid-body fitting tool using spherical harmonics