On the rotational operators in protein structure simulations
On the rotational operators in protein structure simulations
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DOI：
10.1093/protein/gzg092
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发表时间：
2003-10-01
期刊：
影响因子：
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通讯作者：
Kazerounian, K
中科院分区：
文献类型：
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作者：
Alvarado, C;Kazerounian, K
降低处理蛋白质结构分析和构象预测的算法的计算复杂度是至关重要的。大多数这些算法中的一个共同元素是使用旋转操作符在蛋白质中原子的二面角和笛卡尔坐标之间转换几何信息的过程。在文献中，蛋白质结构中使用的运算符是旋转矩阵、矢量和矩阵形式的四元数以及Rodrigues-Gibbs公式。在蛋白质结构相关文献中，推广最广泛的旋转算符是四元数算符。在这项工作中，我们研究了上述旋转算子应用于蛋白质结构的数学运算的计算效率。一项类似的研究应用于蛋白质结构之前还没有报道。我们的结论是，这些旋转算符应用于蛋白质链的计算效率不同于已报道的用于其他应用(如机械)的计算效率，并且结论也不相似。旋转矩阵是蛋白质链中最有效的数学运算符。我们检查了我们在两个蛋白质分子：AB1酪氨酸激酶和肝素结合生长因子2中的发现。我们发现旋转矩阵操作符的数学运算比其他旋转操作符少2%到187%。
The reduction of the computational complexity of the algorithms dealing with protein structure analysis and conformation predictions is of prime importance. One common element in most of these algorithms is the process of transforming geometrical information between dihedral angles and Cartesian coordinates of the atoms in the protein using rotational operators. In the literature, the operators used in protein structures are rotation matrices, quaternions in vector and matrix forms and the Rodrigues-Gibbs formula. In the protein structure-related literature, the most widely promoted rotational operator is the quaternions operator. In this work, we studied the computational efficiency of the mathematical operations of the above rotational operators applied to protein structures. A similar study applied to protein structures has not been reported previously. We concluded that the computational efficiency of these rotational operators applied to protein chains is different from those reported for other applications (such as mechanical machinery) and the conclusions are not analogous. Rotation matrices are the most efficient mathematical operators in the protein chains. We examined our findings in two protein molecules: Ab1 tyrosine kinase and heparin-binding growth factor 2. We found that the rotation matrix operator has between 2 and 187% fewer mathematical operations than the other rotational operators.