Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains
Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains
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DOI：
10.1016/j.molimm.2008.05.022
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发表时间：
2008-08-01
影响因子：
3.6
通讯作者：
Martin, Andrew C. R.
中科院分区：
文献类型：
--
作者：
Abhinandan, K. R.;Martin, Andrew C. R.
在分析蛋白质序列和结构时，标准化的编号方案允许在不进行明确比对的情况下对特征进行比较。这在抗体的情况中已被证明特别有价值。最广泛使用的方案（卡巴特：基于序列；乔西亚：基于结构）仅在互补决定区（CDR）的编号上有所不同。我们分析了广泛使用的卡巴特数据库中的编号注释，发现大约10%的条目包含错误或不一致之处。在结构背景下对序列比对的进一步分析表明，卡巴特和乔西亚方案中一些框架区的插入位点是不正确的。因此，我们提出了乔西亚方案的一个修正版本，它在整个CDR和框架区在结构上都是正确的。为了进行这项分析，我们开发并提供了一种工具，用于自动应用卡巴特、乔西亚和修正的乔西亚编号方案，并仔细地对该工具的性能进行了基准测试。（C）2008爱思唯尔有限公司。保留所有权利。
In analysing protein sequence and structure, standardized numbering schemes allow comparison of features without explicit alignment. This has proved particularly valuable in the case of antibodies. The most widely used schemes (Kabat: sequence-based; Chothia: structure-based) differ only in the numbering of the complementarity determining regions (CDRs). We have analyzed the numbered annotations in the widely used Kabat database and found that approximately 10% of entries contain errors or inconsistencies. Further analysis of sequence alignments in the context of structure suggest that the sites of the insertions in some framework regions in the Kabat and Chothia schemes are incorrect. We therefore propose a corrected version of the Chothia scheme which is structurally correct throughout the CDRs and frameworks. To perform this analysis, we have developed, and made available, a tool for the automatic application of Kabat, Chothia and modified-Chothia numbering schemes and have carefully benchmarked the performance of this tool. (C) 2008 Elsevier Ltd. All rights reserved.