Wei L, Huang E S, Altman R B
Stanford Medical Informatics, Stanford University School of Medicine, CA 94305-5479, USA.
Structure. 1999 Jun 15;7(6):643-50. doi: 10.1016/s0969-2126(99)80085-9.
A principal goal of structure prediction is the elucidation of function. We have studied the ability of computed models to preserve the microenvironments of functional sites. In particular, 653 model structures of a calcium-binding protein (generated using an ab initio folding protocol) were analyzed, and the degree to which calcium-binding sites were recognizable was assessed.
While some model structures preserve the calcium-binding microenvironments, many others, including some with low root mean square deviations (rmsds) from the crystal structure of the native protein, do not. There is a very weak correlation between the overall rmsd of a structure and the preservation of calcium-binding sites. Only when the quality of the model structure is high (rmsd less than 2 A for atoms in the 7 A local neighborhood around calcium) does the modeling of the binding sites become reliable.
Protein structure prediction methods need to be assessed in terms of their preservation of functional sites. High-resolution structures are necessary for identifying binding sites such as calcium-binding sites.
结构预测的一个主要目标是阐明功能。我们研究了计算模型保留功能位点微环境的能力。具体而言，分析了一个钙结合蛋白的653个模型结构（使用从头折叠协议生成），并评估了钙结合位点的可识别程度。
虽然一些模型结构保留了钙结合微环境，但许多其他结构，包括一些与天然蛋白质晶体结构的均方根偏差（rmsds）较低的结构，却没有。结构的整体均方根偏差与钙结合位点的保留之间存在非常微弱的相关性。只有当模型结构的质量很高时（钙周围7埃局部邻域内原子的均方根偏差小于2埃），结合位点的建模才变得可靠。
蛋白质结构预测方法需要根据其对功能位点的保留情况进行评估。高分辨率结构对于识别诸如钙结合位点等结合位点是必要的。
