Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition
Modeling protein-protein, protein-peptide, and protein-oligosaccharide complexes: CAPRI 7th edition
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DOI：
10.1002/prot.25870
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发表时间：
2020-01-10
影响因子：
2.9
通讯作者：
Wodak, Shoshana J.
中科院分区：
文献类型：
--
作者：
Lensink, Marc F.;Nadzirin, Nurul;Wodak, Shoshana J.
我们提出了第七份报告的性能的方法预测的原子分辨率结构的蛋白质复合物提供的目标，以社区范围内的倡议预测相互作用的关键评估。基于57个团体提交的36114个蛋白质复合物模型（包括13个自动服务器），对2016年至2019年期间举行的8个蛋白质-蛋白质，3个蛋白质-肽和5个具有不同长度配体的蛋白质-寡糖靶标的预测轮进行了性能评估。六个蛋白质-蛋白质靶点代表了具有挑战性的杂合复合物，这是由于诸如单个亚基或完整复合物的远亲模板的可用性、结构域间灵活性、结合区域的构象调整或复合物的多组分性质等因素。蛋白质-肽和蛋白质-寡糖复合物的主要挑战是精确地模拟配体构象及其在界面处的相互作用。令人鼓舞的是，获得了总共六种蛋白质-蛋白质复合物的可接受质量或更好的模型，其中包括四种具有挑战性的杂合复合物和一种同源十聚体。但这些目标中很少有预测具有中等或更高的准确性。获得了三个蛋白质-肽靶标中的两个和蛋白质-寡糖靶标中的一个的高精度模型。其余的蛋白质-糖靶标以中等准确度预测。我们的分析表明，在预测日益具有挑战性和多样化的目标类型的进展是由于基于模板的建模技术与对接，评分和模型优化程序的更紧密的集成，并在基础方法的显着增量改进。
We present the seventh report on the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions. Performance was evaluated on the basis of 36 114 models of protein complexes submitted by 57 groups-including 13 automatic servers-in prediction rounds held during the years 2016 to 2019 for eight protein-protein, three protein-peptide, and five protein-oligosaccharide targets with different length ligands. Six of the protein-protein targets represented challenging hetero-complexes, due to factors such as availability of distantly related templates for the individual subunits, or for the full complex, inter-domain flexibility, conformational adjustments at the binding region, or the multi-component nature of the complex. The main challenge for the protein-peptide and protein-oligosaccharide complexes was to accurately model the ligand conformation and its interactions at the interface. Encouragingly, models of acceptable quality, or better, were obtained for a total of six protein-protein complexes, which included four of the challenging hetero-complexes and a homo-decamer. But fewer of these targets were predicted with medium or higher accuracy. High accuracy models were obtained for two of the three protein-peptide targets, and for one of the protein-oligosaccharide targets. The remaining protein-sugar targets were predicted with medium accuracy. Our analysis indicates that progress in predicting increasingly challenging and diverse types of targets is due to closer integration of template-based modeling techniques with docking, scoring, and model refinement procedures, and to significant incremental improvements in the underlying methodologies.