Protein‐protein docking plays an important role in the computational prediction of the complex structure between two proteins. For years, a variety of docking algorithms have been developed, as witnessed by the critical assessment of prediction interactions (CAPRI) experiments. However, despite their successes, many docking algorithms often require a series of manual operations like modeling structures from sequences, incorporating biological information, and selecting final models. The difficulties in these manual steps have significantly limited the applications of protein‐protein docking, as most of the users in the community are nonexperts in docking. Therefore, automated docking like a web server, which can give a comparable performance to human docking protocol, is pressingly needed. As such, we have participated in the blind CAPRI experiments for Rounds 38‐45 and CASP13‐CAPRI challenge for Round 46 with both our HDOCK automated docking web server and human docking protocol. It was shown that our HDOCK server achieved an “acceptable” or higher CAPRI‐rated model in the top 10 submitted predictions for 65.5% and 59.1% of the targets in the docking experiments of CAPRI and CASP13‐CAPRI, respectively, which are comparable to 66.7% and 54.5% for human docking protocol. Similar trends can also be observed in the scoring experiments. These results validated our HDOCK server as an efficient automated docking protocol for nonexpert users. Challenges and opportunities of automated docking are also discussed.

中文翻译：

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自动化蛋白质-蛋白质对接的挑战和机遇：CAPRI第38-46轮中的HDOCK服务器与人类预测。

蛋白质-蛋白质对接在两个蛋白质之间复杂结构的计算预测中起着重要作用。多年来，已开发出各种对接算法，如对预测交互作用的关键评估（CAPRI）实验所证明。然而，尽管取得了成功，但许多对接算法通常仍需要一系列手动操作，例如根据序列对结构进行建模，合并生物学信息以及选择最终模型。这些手动步骤中的困难极大地限制了蛋白质-蛋白质对接的应用，因为该社区中的大多数用户都不是对接专家。因此，迫切需要像Web服务器这样的自动对接，它可以提供与人类对接协议相当的性能。因此，我们已经通过HDOCK自动对接网络服务器和人工对接协议参与了第38至45轮盲CAPRI实验和第46轮CASP13-CAPRI挑战竞赛。结果表明，在CAPRI和CASP13-CAPRI的对接实验中，我们的HDOCK服务器在提交的前10个预测中分别对目标的65.5％和59.1％的目标实现了“可接受”或更高的CAPRI评估模型，与人体对接方案分别为66.7％和54.5％。在评分实验中也可以观察到类似的趋势。这些结果验证了我们的HDOCK服务器是针对非专家用户的高效自动对接协议。还讨论了自动对接的挑战和机遇。结果表明，在CAPRI和CASP13-CAPRI的对接实验中，我们的HDOCK服务器在提交的前10个预测中分别对目标的65.5％和59.1％的目标实现了“可接受”或更高的CAPRI评估模型，与人体对接方案分别为66.7％和54.5％。在评分实验中也可以观察到类似的趋势。这些结果验证了我们的HDOCK服务器是针对非专家用户的高效自动对接协议。还讨论了自动对接的挑战和机遇。结果表明，在CAPRI和CASP13-CAPRI的对接实验中，我们的HDOCK服务器在提交的前10个预测中分别对目标的65.5％和59.1％的目标实现了“可接受”或更高的CAPRI评估模型，与人体对接方案分别为66.7％和54.5％。在评分实验中也可以观察到类似的趋势。这些结果验证了我们的HDOCK服务器是针对非专家用户的高效自动对接协议。还讨论了自动对接的挑战和机遇。在评分实验中也可以观察到类似的趋势。这些结果验证了我们的HDOCK服务器是针对非专家用户的高效自动对接协议。还讨论了自动对接的挑战和机遇。在评分实验中也可以观察到类似的趋势。这些结果验证了我们的HDOCK服务器是针对非专家用户的高效自动对接协议。还讨论了自动对接的挑战和机遇。