Theobald Douglas L
Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA.
Acta Crystallogr A. 2005 Jul;61(Pt 4):478-80. doi: 10.1107/S0108767305015266. Epub 2005 Jun 23.
A common measure of conformational similarity in structural bioinformatics is the minimum root mean square deviation (RMSD) between the coordinates of two macromolecules. In many applications, the rotations relating the structures are not needed. Several common algorithms for calculating RMSDs require the computationally costly procedures of determining either the eigen decomposition or matrix inversion of a 3x3 or 4x4 matrix. Using a quaternion-based method, here a simple algorithm is developed that rapidly and stably determines RMSDs by circumventing the decomposition and inversion problems.
结构生物信息学中构象相似性的一种常用度量是两个大分子坐标之间的最小均方根偏差（RMSD）。在许多应用中，并不需要确定结构之间的旋转关系。几种计算RMSD的常用算法需要通过计算代价高昂的过程来确定3×3或4×4矩阵的特征分解或矩阵求逆。本文利用基于四元数的方法开发了一种简单算法，该算法通过规避分解和求逆问题来快速稳定地确定RMSD。
