Overview
Biomolecular Docking
Once we know that two proteins interact, it is important to understand how they bind. Predicting the structure of the complex formed by two molecules is referred to as the docking problem. Docking was initially described as a "lock and key mechanism", in which the configuration of the molecules involved in the complex did not change upon binding. The problem was then only to find a rigid body transformation that brings the two molecules into their correct orientations. It is now established that most molecules change conformation upon binding, leading to an induced fit. Predicting docking that include flexibility of all molecular actors involved in the assembly remains a difficult problem.
In this chapter, we provide an overview of binding and docking. Fourier-based methods for docking are presented. We also describe two well establihed docking programs, DOCK and DARWIN.
Experiments
