Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing, China.
PLoS One. 2011 Apr 28;6(4):e19238. doi: 10.1371/journal.pone.0019238.
The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the -to- atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. The AES model eliminates about 95% of the incorrectly counted contact-pairs in the ISS model. Algorithm analysis shows that AES model is the most computational intensive while ADC model has moderate computational cost. We derived a dataset of the mis-estimated contact pairs by AES model. The most misjudged pairs are Arg-Glu, Arg-Asp and Arg-Tyr. Such a dataset can be useful for developing the improved AES model by incorporating the pair-specific information for the cutoff distance.
确定残基接触的标准是从蛋白质结构中推导出基于知识的均方力势能计算的一个基本问题。常用的标准是要求侧链中心到中心的距离或 -to-原子距离在预定的截止距离内。然而，侧链的空间各向异性决定了识别接触对具有挑战性。本研究比较了三种侧链接触模型：原子距离标准（ADC）模型、各向同性球体侧链（ISS）模型和各向异性椭球体侧链（AES）模型，使用了蛋白质数据库中的 424 个高分辨率蛋白质结构。结果表明，ADC 模型最准确，ISS 模型最差。AES 模型消除了 ISS 模型中约 95%的错误计数的接触对。算法分析表明，AES 模型计算最密集，而 ADC 模型的计算成本适中。我们通过 AES 模型得到了一个误判接触对的数据集。最容易被误判的对是 Arg-Glu、Arg-Asp 和 Arg-Tyr。这样的数据集对于通过结合对特定的截止距离信息来开发改进的 AES 模型可能是有用的。
