Protein-protein docking is a method for predicting the protein complex structure from monomeric protein structures. Because protein structural information has been increased and the application field has been expanded to more difficult ones such as interactome prediction, a faster protein-protein docking method has been eagerly demanded. MEGADOCK is fast protein-protein ...

We propose a new hydrophobic interaction model that applies atomic contact energy for our protein---protein docking software, MEGADOCK. Previously, this software used only two score terms, shape complementarity and electrostatic interaction. We develop a modified score function incorporating the hydrophobic interaction effect. Using the proposed score function, MEGADOCK can calculate ...