Bounding volumes for proteins: a comparative study.

A chain tree is a data structure for representing changing protein conformations. It enables very fast detection of clashes and free potential energy calculations. The efficiency of chain trees is closely related to the bounding volumes associated with chain tree nodes. A protein subchain associated with a node of a chain tree will clash with another subchain only if their bounding volumes intersect. It is therefore essential that bounding volumes are as tight as possible while intersection tests can be carried out efficiently. We compare the performance of four different types of bounding volumes in connection with the rotation of protein bonds. It is observed that oriented bounding boxes are not as good as could be expected judging by their extensive use in various applications. Both rectangular- and line-swept spheres are shown to have very good tightness of fit but the line-swept, or even simple spheres, are shown to be significantly faster because of quick overlap checks. We also investigate how the performance of the recently introduced adjustable chain trees is affected by different bounding volume types.