Benchmarking of dimeric threading and structure refinement
Benchmarking of dimeric threading and structure refinement
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DOI：
10.1002/prot.20878
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发表时间：
2006-05-15
影响因子：
2.9
通讯作者：
Skolnick, J
中科院分区：
文献类型：
--
作者：
Grimm, V;Zhang, Y;Skolnick, J
蛋白质相互作用的理解是后基因组时代的一个主要目标。因此，从序列预测相互作用和随后产生的全长二聚体模型是非常感兴趣的，特别是因为结构特征的蛋白质-蛋白质复合物的数量很少。由170个弱同源二聚体靶模板对的基准的质量评估。它们在两步法中预测，类似于先前描述的MULTI-PROSPECTOR算法：通过线程将每个靶序列分配给单体模板结构;然后，选择属于相同物理相互作用二聚体模板的那些模板。此外，我们使用结构比对作为“金标准”来评估正确分配的单体和二聚体模板的百分比，并评估线程结果，重点是界面区域的比对质量。这项工作的目的是给二聚体线程的质量的定量图片。除了一个之外，所有单体模板都被正确识别，但大约40%的二聚体模板仍然是有问题的或不正确的。用TASSER方法生成的三个全长二聚体模型的初步结果显示，平均而言，最终模型比初始模板有显著改善。
The understanding of protein-protein interactions is a major goal in the post-genomic era. The prediction of interaction from sequence and the subsequent generation of full-length dimeric models is therefore of great interest especially because the number of structurally characterized protein-protein complexes is sparse. A quality assessment of a benchmark comprised of 170 weakly homologous dimeric target-template pairs is presented. They are predicted in a two-step method, similar to the previously described MULTI-PROSPECTOR algorithm: each target sequence is assigned to a monomeric template structure by threading; then, those templates that belong to the same physically interacting dimer template are selected. Additionally we use structural alignments as the "gold standard" to assess the percentage of correctly assigned monomer and dimer templates and to evaluate the threading results with a focus on the quality of the alignments in the interfacial region. This work aims to give a quantitative picture of the quality of dimeric threading. Except for one, all monomer templates are identified correctly, but approximately 40% of the dimer templates are still problematic or incorrect. Preliminary results for three full-length dimeric models generated with the TASSER method show on average a significant improvement of the final model over the initial template.