Complementarity of ligand flexibility and protein flexibility
Charge sharing between ligand and biomolecule as it impacts binding
Locating novel pockets/sub-pockets of high interaction energy, druggability
*"Diverse Fragment Clustering and Water Exclusion Identify Protein Hot Spots" Kulp et al. JACS 2011 133(28), 10740-10743.
Estimate of binding affinity (free energy) and rank-ordering
Accurate predictions based on annealing of chemical potential in a Grand Canonical Monte Carlo simulation
**“A fragment-based approach to the SAMPL3 Challenge” Kulp at al. J Comput. Aided Mol Des. 2012 26(5), 583-94.