Department of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States.
J Phys Chem B. 2012 Oct 18;116(41):12501-9. doi: 10.1021/jp307741u. Epub 2012 Oct 4.
Structural properties of over 55 small proteins have been determined using both density-based and wave-function-based electronic structure methods in order to assess the ability of ab initio "force fields" to retain the properties described by experimental structures measured with crystallography or nuclear magnetic resonance. The efficiency of the GPU-based quantum chemistry algorithms implemented in our TeraChem program enables us to carry out systematic optimization of ab initio protein structures, which we compare against experimental and molecular mechanics force field references. We show that the quality of the ab initio optimized structures, as judged by conventional protein health metrics, increases with increasing basis set size. On the other hand, there is little evidence for a significant improvement of predicted structures using density functional theory as compared to Hartree-Fock methods. Although occasional pathologies of minimal basis sets are observed, these are easily alleviated with even the smallest double-ζ basis sets.
为了评估从头算“力场”保留实验结构所描述性质的能力，我们使用基于密度和基于波函数的电子结构方法来确定超过 55 个小蛋白的结构性质。我们的 TeraChem 程序中基于 GPU 的量子化学算法的效率使我们能够对从头算蛋白结构进行系统优化，并将其与实验和分子力学力场参考进行比较。我们表明，根据常规蛋白健康指标判断，从头算优化结构的质量随着基组大小的增加而提高。另一方面，与 Hartree-Fock 方法相比，使用密度泛函理论预测结构几乎没有明显改善的证据。尽管偶尔会观察到最小基组的病理现象，但即使使用最小的双ζ基组也很容易缓解这些问题。
