Clore G M, Nilges M, Brünger A T, Karplus M, Gronenborn A M
FEBS Lett. 1987 Mar 23;213(2):269-77. doi: 10.1016/0014-5793(87)81504-1.
A direct comparison of the metric matrix distance geometry and restrained molecular dynamics methods for determining three-dimensional structures of proteins on the basis of interproton distances is presented using crambin as a model system. It is shown that both methods reproduce the overall features of the secondary and tertiary structure (shape and polypeptide fold). The region of conformational space sampled by the converged structures generated by the two methods is similar in size, and in both cases the converged structures are distributed about mean structures which are closer to the X-ray structure than any of the individual structures. The restrained molecular dynamics structures are superior to those obtained from distance geometry as regards local backbone conformation, side chain positions and non-bonding energies.
以胰凝乳蛋白酶抑制剂作为模型系统，对基于质子间距离测定蛋白质三维结构的度量矩阵距离几何方法和受限分子动力学方法进行了直接比较。结果表明，这两种方法都能再现二级和三级结构的整体特征（形状和多肽折叠）。两种方法生成的收敛结构所采样的构象空间区域大小相似，并且在这两种情况下，收敛结构都围绕着平均结构分布，这些平均结构比任何单个结构都更接近X射线结构。在局部主链构象、侧链位置和非键能方面，受限分子动力学结构优于从距离几何方法获得的结构。
