Methodological areas of interest are incorporation into DOCK of on-the-fly ligand minimization and energy function improvements, such as a geometry dependent hydrogen bond term, and explicit accounting for covalent bond energy. Systematic analysis of covalent complex structures provides us with: 1. A gold standard benchmark for the pose prediction of covalent adducts. 2. Knowledge based statistics derived from known complexes that can be implemented as energy function improvements. These improvements will continually be put to the test via prospective predictions and experimental testing on the lab's model systems and other systems in the future.
