Fig 1. Addition of information to augment template-based modeling and ligand docking protocols.

Sequence → Structure Beginning with a target sequence, apo protein structures can be predicted. The accuracy of these models has been shown to increase with the addition of other sources of information, including accurate sequence-structure mappings (alignments) [13], familial (evolutionary) constraints [14], multiple templates [15] and fragments [16] Structure → Docked Structure Taking the apo structure and docking a ligand into results in a docked structure, with a ligand bound. The accuracy of these models has been shown to increase with the addition of ligand conformational degrees of freedom and chemical mechanism constraints. By adding CG constraints, we measure the increase in accuracy over the entire pipeline.