Doing a good turn: the use of quaternions for rotation in molecular docking

Much work has been done on algorithms for structure-based drug modeling in silico, and almost all these systems have a core need for three-dimensional geometric models. The manipulation of these models, particularly their transformation from one position to another, is a substantial computational task with design questions of its own. Solid body rotation is an important part of these transformations, and we present here a careful comparison of two established techniques: Euler angles and quaternions. The relative superiority of the quaternion method when applied to molecular docking is demonstrated by practical experiment, as is the crucial importance of proper adjustment calculations in search methods.