Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur, 25-28 rue du Dr. Roux, Paris 75724, France.
Proteins. 2011 May;79(5):1525-37. doi: 10.1002/prot.22980. Epub 2011 Mar 1.
The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal choices for potential shape (bounds-free log-harmonic shape) and restraints weights. We compare the classical protocol with the Bayesian approach for more than 300 protein structures. We analyze the conformation similarity to the corresponding X-ray crystal structure, the distribution of the conformations around their average, and independent validation criteria. On average, the log-harmonic potential reduces the difference to the X-ray crystal structure. If the log-harmonic potential is used, the constant weighting tightens the distribution around the average conformation, with respect to the distributions obtained with Bayesian weighting. Conversely, the structure quality is improved by the Bayesian weighting over the classical procedure, whereas constant weighting worsens some criteria. The quality improvement obtained with the log-harmonic potential coupled to Bayesian weighting validates this approach on a representative set of protein structures.
经典的核磁共振结构计算方法分配经验距离范围，并使用历史权重因子。然而，贝叶斯分析表明，对于潜在形状（无界对数调和形状）和约束权重，存在更优的选择。我们比较了 300 多个蛋白质结构的经典方案和贝叶斯方法。我们分析了与相应 X 射线晶体结构的构象相似性、构象在平均值周围的分布以及独立的验证标准。平均而言，对数调和势降低了与 X 射线晶体结构的差异。如果使用对数调和势，则常数权重会使构象分布在平均构象周围收紧，相对于使用贝叶斯权重获得的分布。相反，贝叶斯权重相对于经典过程提高了结构质量，而常数权重则会恶化某些标准。将对数调和势与贝叶斯权重相结合的方法在一组有代表性的蛋白质结构上验证了这种方法。
