INSERM UMR-S 973/Université Paris Diderot/Sorbonne Paris Cité/RPBS, Paris 75205, France.
Physik T38, Technische Universität München, Garching 85748, Germany.
Nucleic Acids Res. 2017 Jul 3;45(W1):W361-W364. doi: 10.1093/nar/gkx335.
Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets. Its performance is similar or better than state-of-the-art local docking protocols that do require binding site information. Here we present a novel web server that carries out the rigid-body stage of pepATTRACT. On the peptiDB benchmark, the web server generates a correct model in the top 50 in 34% of the cases. Compared to the full pepATTRACT protocol, this leads to some loss of performance, but the computation time is reduced from ∼18 h to ∼10 min. Combined with the fact that it is fully blind, this makes the web server well-suited for large-scale in silico protein-peptide docking experiments. The rigid-body pepATTRACT server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT.
肽-蛋白相互作用在细胞中普遍存在，并构成相互作用组的重要组成部分。计算对接方法可以补充这些复合物的实验表征，但目前的方案不适用于蛋白质组规模。pepATTRACT 是一种新型的对接方案，完全是盲目的，即它不需要任何关于结合位点的信息。在其开发的各个阶段，pepATTRACT 都参加了 CAPRI，成功预测了七个蛋白-肽靶标中的五个。它的性能与需要结合位点信息的最先进的局部对接方案相似或更好。这里我们介绍了一个新的网页服务器，它执行 pepATTRACT 的刚体阶段。在 peptiDB 基准测试中，网页服务器在 34%的情况下生成了前 50 名中的正确模型。与完整的 pepATTRACT 方案相比，这导致了一些性能损失，但计算时间从约 18 小时减少到约 10 分钟。由于它是完全盲目的，这使得网页服务器非常适合大规模的计算蛋白质-肽对接实验。刚体 pepATTRACT 服务器可在 http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT 上免费获得。
