Chen Z, Blanc E, Chapman M S
Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.
Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):464-8. doi: 10.1107/s090744499801097x.
Real-space targets and molecular-dynamics search protocols have been combined to improve the convergence of macromolecular atomic refinement. This was accomplished by providing a local real-space target function for the molecular-dynamics program X-PLOR. With poor isomorphous replacement experimental phases, molecular dynamics does not improve real-space refinement. However, with high-quality anomalous diffraction phases convergence is improved at the start of refinement, and torsion-angle real-space molecular dynamics performs better than other available least-squares or maximum-likelihood methods in real or reciprocal space. It is shown that the improvements result from an optimization method that can escape local minima and from a reduction of overfitting through the implicit use of phases and through use of a local refinement in which errors in remote parts of the structure cannot be mutually compensating.
实空间目标函数与分子动力学搜索协议相结合，以提高大分子原子精修的收敛性。这是通过为分子动力学程序X-PLOR提供一个局部实空间目标函数来实现的。在同晶置换实验相位较差的情况下，分子动力学并不能改善实空间精修。然而，在高质量反常衍射相位的情况下，精修开始时收敛性得到改善，并且扭转角实空间分子动力学在实空间或倒易空间中比其他可用的最小二乘法或最大似然法表现更好。结果表明，这些改进源于一种能够逃离局部最小值的优化方法，以及通过隐式使用相位和通过使用局部精修来减少过拟合，在局部精修中结构远程部分的误差不能相互补偿。
