Protien Threading Methods for a Conserved Domain Database

我们已经开发出计算机方法，将蛋白质的序列与结构数据库中的“折叠”库进行比较。序列通过不同的结构被“穿线”，那些最相容的结构通过使用接触电势的能量计算来识别。由于它们直接检测结构相似性，线性化方法可以识别通过序列比较可能无法检测到的非常遥远的进化关系。今年的研究集中在核心元素线性化方法的测试、盲预测和控制实验中，以及提高灵敏度的算法改进上。使用已知结构的对照实验确定了成功折叠识别和准确建模的阈值：类似的“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埃或更少的残留量，以便保留大部分接触。对1996年CASP2讲习班(结构预测的关键评估)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，结构相似性可能不那么广泛，已经考虑了几个提高敏感度的改进。数据库结构的“核心”的新定义，根据与已知结构的同源基因中可重叠的区域，已被证明可以减少线程预测中的假阴性。接触电势和序列基序分数的组合也被证明在困难的识别问题中提高了敏感度。使用严格的p值计算被证明可以减少假阳性。有了这些改进，折叠识别有望可靠地检测到更大比例的遥远进化关系。这一点在1998年的CASP3研讨会上得到了证明，在参加比赛的90多个国际团体中，NCBI团队被授予Fold认可的“第一名”。本项目开发的线程化方法目前正被应用于构建保守结构域数据库(CDD)。将来自序列比较的种子结构域比对映射到已知的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。这些比对通过线程计算来验证，并且通过PSI-BLAST扫描检测到的附加代表性序列通过线程被合并到比对中。CDD比对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结构域很容易识别，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。

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 this year 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 PSI-BLAST scanning are merged into the alignment by threading. CDD alignments serve as a protein classification system for public information retrieval 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.