Alignment Methods For A Conserved Domain Database

我们已经开发了计算机方法，将蛋白质序列与结构数据库中的“折叠”库进行比较。这个序列通过不同的结构被“串联”起来，那些最相容的结构通过能量计算来识别，使用接触势。由于它们直接检测结构相似性，线程方法可以识别通过序列比较无法检测到的非常遥远的进化关系。研究主要集中在核心元素线程方法的测试，盲预测和控制实验，以及算法改进以提高灵敏度。使用已知结构的控制实验确定了成功折叠识别和准确建模的阈值：相似的“核心”亚结构必须包含60%或更多的蛋白质，并且必须重叠到2.5埃或更小的残差，这样才能保留大部分接触。1996年CASP2研讨会（结构预测关键评估）的预测分析证实了这一结论。然而，在某些远距离关系的情况下，结构相似性可以不那么广泛，并且已经考虑了几种提高灵敏度的改进方法。数据库结构的“核心”的新定义，根据在同源物中与已知结构重叠的区域，已被证明可以减少线程预测中的假阴性。接触电位与序列基序评分的结合也显示出在困难的识别问题中增加敏感性。使用严格的p值计算被证明可以减少误报。有了这些改进，折叠识别有望可靠地检测出更大比例的远距离进化关系。这在1998年的CASP3研讨会上得到了证明，NCBI团队在90多个参加比赛的国际团队中获得了“第一名”。本课题开发的线程化方法目前正应用于保守域数据库（CDD）的构建。从序列比较中得到的种子结构域比对，被映射到已知的3D结构上，并与3D结构比对进行比较，以定义代表性结构域样本的核心结构比对。通过线程计算验证这些比对，并通过线程将RPS-BLAST扫描检测到的其他代表性序列合并到比对中。一种新开发的使用核心-元件“块”的序列与PSSM（位置特定评分矩阵）比对算法大大加快了这些计算速度，并使核心-元件比对成为构建蛋白结构域比对的实用工具。CDD比对可作为公共信息检索服务的蛋白质分类系统。具有保守结构和功能的域很容易被识别，结果序列/结构比对的可视化提供了结构-功能关系的详细注释。今年的工作重点是构建CDTree对齐层次编辑系统。版本1和版本2已经部署到CDD管理团队，预计将于明年向公众发布。

We have developed computer methods to compare a protein's sequence with a library of "folds" from the structural database. The sequence is "threaded" through alternative structures, and those most compatible are identified by energy calculations, using contact potentials. Since they directly detect structural similarity, threading methods can identify very distant evolutionary relationships that may be undetectable by sequence comparison. Research has focused on testing of the core-element threading method, in blind predictions and control experiments, and on algorithmic improvements to increase sensitivity. Control experiments using known structures identified thresholds for successful fold recognition and accurate modeling: the similar "core" substructure must comprise 60% or more of the protein and must superpose to a residual of 2.5 Angstroms or less, such that a large fraction of contacts are preserved. Analysis of predictions for the 1996 CASP2 workshop (Critical Assessment of Structure Prediction) confirmed this conclusion. Structural similarity can be less extensive in some cases of distant relationship, however, and several improvements to increase sensitivity have been considered. New definitions of the "core" of database structures, according to the regions superimposable in homologs with known structures, has been show to reduce false negatives in threading predictions. Combination of contact potentials with sequence-motif scores was also shown to increases sensitivity in difficult recognition problems. Use of rigorous p-value calculations was shown to reduce false positives. With these improvements fold recognition may be expected to reliably detect a greater proportion of the distant evolutionary relationships. This has been demonstrated at the 1998 CASP3 workshop, where the NCBI team was awarded "first place" in fold recognition, among over 90 international groups entering the competition. The threading methods developed in this project are now being applied to construction of a conserved domain database (CDD). Seed domain alignments, derived from sequence comparison, are mapped onto known 3D structures and compared to 3D structure alignments, to define a core-structure alignment for a sample of representative domains. These alignments are validated by threading calculations, and additional representative sequences detected by RPS-BLAST scanning are merged into the alignment by threading. A newly developed algorithm for sequence vs. PSSM (position specific score matrix) alignment using core-element "blocks" has greatly speeded these calculations, and made core-element alignment into a practical tool for construction of curated protein domain alignments. CDD alignments serve as a protein classification system for public information retreival services. Domains with conserved structure and function are easily identified, and visualization of the resulting sequence/structure alignments provides a detailed annotation of structure-function relationships. Work this year has focussed on construction of the CDTree alignment heirarchy editing system. Versions 1 and then 2 were deployed to the CDD curation team, and release to the public is anticipated next year.