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VORFFIP-Driven Dock: V-D²OCK, a Fast and Accurate Protein Docking Strategy

机译:VORFFIp驱动的底座:V-D²OCK,一种快速准确的蛋白质对接策略

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摘要

The experimental determination of the structure of protein complexes cannot keep pace with the generation of interactomic data, hence resulting in an ever-expanding gap. As the structural details of protein complexes are central to a full understanding of the function and dynamics of the cell machinery, alternative strategies are needed to circumvent the bottleneck in structure determination. Computational protein docking is a valid and valuable approach to model the structure of protein complexes. In this work, we describe a novel computational strategy to predict the structure of protein complexes based on data-driven docking: VORFFIP-driven dock (V-D²OCK). This new approach makes use of our newly described method to predict functional sites in protein structures, VORFFIP, to define the region to be sampled during docking and structural clustering to reduce the number of models to be examined by users. V-D²OCK has been benchmarked using a validated and diverse set of protein complexes and compared to a state-of-art docking method. The speed and accuracy compared to contemporary tools justifies the potential use of VD²OCK for high-throughput, genome-wide, protein docking. Finally, we have developed a web interface that allows users to browser and visualize V-D²OCK predictions from the convenience of their web-browsers.
机译:蛋白质复合物结构的实验确定无法与相互作用组数据的产生保持同步,因此导致差距不断扩大。由于蛋白质复合物的结构细节对于全面了解细胞机制的功能和动力学至关重要,因此需要其他策略来规避结构确定中的瓶颈。计算蛋白质对接是一种有效且有价值的建模蛋白质复合物结构的方法。在这项工作中,我们描述了一种基于数据驱动对接的预测蛋白质复合物结构的新颖计算策略:VORFFIP驱动对接(V-D²OCK)。这种新方法利用我们最新描述的方法来预测蛋白质结构中的功能位点VORFFIP,以定义在对接和结构聚类期间要采样的区域,以减少用户要检查的模型数量。 V-D²OCK已使用一组经过验证的多样化蛋白质复合物进行了基准测试,并与最先进的对接方法进行了比较。与现代工具相比,速度和准确性证明了VD²OCK在高通量,全基因组蛋白对接中的潜在用途。最后,我们开发了一个Web界面,允许用户从其Web浏览器的便利性中浏览和可视化V-D²OCK预测。

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