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首页> 外文期刊>Journal of Molecular Biology >An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance.
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An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance.

机译：蛋白质序列和结构分析和建模的综合方法。 I.蛋白质结构比对和蛋白质结构距离的定量测量。

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摘要

We have devised and implemented in PrISM (protein informatics system for modeling) a new measure of protein structural relationships, the protein structural distance (PSD). The PSD is designed to describe relationships between protein structures in quantitative rather than descriptive terms and is applicable both when two structures are very similar, and when they are very different. It is calculated with a structural alignment procedure that uses double dynamic programming to align secondary structure elements and an iterative rigid body superposition that minimizes the root-mean-square deviation of C(alpha) atoms. The alignment algorithm, as implemented on a modest workstation, is computationally efficient, allowing for large-scale structural comparisons. PSD scores for more than one and a half million pairs of proteins were calculated and compared to the discrete classification of proteins in the SCOP database. The PSD scores, which were obtained automatically, are in large part consistent with the manually derived classifications in SCOP. Discrepancies do arise, however, due, in part, to the fact that SCOP uses criteria other than structural similarity to derive classifications while the PrISM procedure is exclusively structure based. Analysis of PSD scores suggests that there is a continuous aspect of protein conformation space, even though various classification schemes are extremely useful. The use of a continuous measure for structural distance between all pairs of proteins allows us, as described in the two accompanying papers to derive sequence/structure relationships in a more quantitative way than has previously been possible. An important strength of the approach implemented in PrISM is its ability to address many different kinds of queries interactively, making its structural comparison procedure a convenient computational tool that complements structural classification databases such as SCOP and CATH. Copyright 2000 Academic Press.
机译：我们已经在PrISM（用于建模的蛋白质信息系统）中设计并实现了一种新的蛋白质结构关系测量方法，即蛋白质结构距离（PSD）。 PSD旨在以定量而非描述性的术语描述蛋白质结构之间的关系，并且在两个结构非常相似以及彼此非常不同时都适用。它是使用结构对齐程序进行计算的，该程序使用双重动态编程来对齐二级结构元素，并使用迭代刚体叠加来最小化Cα原子的均方根偏差。如在适中的工作站上实现的对齐算法，计算效率高，可进行大规模的结构比较。计算了超过一百五十万对蛋白质的PSD得分，并将其与SCOP数据库中蛋白质的离散分类进行比较。 PSD得分是自动获得的，在很大程度上与SCOP中的手动得出的分类一致。但是，确实存在差异，部分原因是由于SCOP使用结构相似性以外的标准来推导分类，而PrISM程序完全基于结构。 PSD分数的分析表明，尽管各种分类方案非常有用，但蛋白质构象空间还是一个连续的方面。使用连续测量所有蛋白质对之间的结构距离，可以使我们如两篇附带的论文所述，以比以前可能的方法更定量的方式得出序列/结构关系。 PrISM中实现的方法的一个重要优势是它可以交互地处理许多不同类型的查询的能力，从而使其结构比较过程成为方便的计算工具，可以补充诸如SCOP和CATH等结构分类数据库。版权所有2000学术出版社。

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