Badger J, Kumar R A, Yip P, Szalma S
Molecular Simulations Inc., San Diego, California, USA.
Proteins. 1999 Apr 1;35(1):25-33.
This article describes new methods for X-ray crystallographic refinement and nuclear magnetic resonance (NMR) structure determination that are available in the recent release of the X-PLOR software, X-PLOR 98.0. The major new features of the X-PLOR 98.0 software are: (i) the introduction of maximum likelihood methods (Pannu and Read, Acta Crystallogr 1996;A52:659-668) for X-ray crystallographic refinement with structure factor amplitude, intensity and phase probability targets, (ii) the addition of the Andersen thermal coupling method for temperature control during simulated annealing refinements, (iii) a new utility function for converting reflection data in to the X-PLOR format, (iv) validated scripts and performance enhancements for structure determination from NMR distance restraints using torsion angle dynamics, (v) fast code for direct nuclear Oberhauser effect (NOE) refinement using matrix doubling and gaussian quadratures, (vi) methodologies for using ambiguous restraint information to perform automated iterative peak assignment and structure determination (Nilges et al., J Mol Biol 1997;269: 408-422). Additional developments in methodology for refining crystal structures from poor initial models include the implementation of a fast adaptive bulk solvent scattering correction and an energy minimization routine that makes use of second derivative information. Trial crystallographic refinements with an energy minimization protocol that includes these enhancements indicate significantly improved convergence. The quality of the resulting models appears comparable to models obtained from refinement protocols that incorporate torsion angle dynamics. Test applications of the new energy minimizer to NMR structure refinement with using NOE calculations also show improved convergence, leading to more optimized final models.
本文介绍了X-PLOR软件最新版本X-PLOR 98.0中可用于X射线晶体学精修和核磁共振（NMR）结构测定的新方法。X-PLOR 98.0软件的主要新特性包括：（i）引入了用于X射线晶体学精修的最大似然法（Pannu和Read，《晶体学报》1996年；A52：659 - 668），其目标为结构因子振幅、强度和相位概率；（ii）在模拟退火精修过程中添加了用于温度控制的安徒生热耦合方法；（iii）一个用于将反射数据转换为X-PLOR格式的新实用函数；（iv）经过验证的脚本以及使用扭转角动力学从NMR距离约束进行结构测定的性能增强；（v）使用矩阵加倍和高斯求积法进行直接核Overhauser效应（NOE）精修的快速代码；（vi）使用模糊约束信息进行自动迭代峰归属和结构测定的方法（Nilges等人，《分子生物学杂志》1997年；269：408 - 422）。从较差的初始模型精修晶体结构的方法的其他进展包括实施快速自适应体溶剂散射校正和利用二阶导数信息 的能量最小化程序。使用包含这些增强功能的能量最小化协议进行的晶体学精修试验表明收敛性显著提高。所得模型的质量似乎与从包含扭转角动力学的精修协议获得的模型相当。将新的能量最小化器应用于使用NOE计算的NMR结构精修的测试应用也显示出收敛性得到改善，从而得到更优化的最终模型。
