Biological and Chemical Research Centre, University of Warsaw.
Faculty of Physics at the University of Warsaw.
Brief Bioinform. 2019 Nov 27;20(6):2299-2305. doi: 10.1093/bib/bby080.
CABS-dock is a computational method for protein-peptide molecular docking that does not require predefinition of the binding site. The peptide is treated as fully flexible, while the protein backbone undergoes small fluctuations and, optionally, large-scale rearrangements. Here, we present a specific CABS-dock protocol that enhances the docking procedure using fragmentary information about protein-peptide contacts. The contact information is used to narrow down the search for the binding peptide pose to the proximity of the binding site. We used information on a single-chosen and randomly chosen native protein-peptide contact to validate the protocol on the peptiDB benchmark. The contact information significantly improved CABS-dock performance. The protocol has been made available as a new feature of the CABS-dock web server (at http://biocomp.chem.uw.edu.pl/CABSdock/).
CABS-dock is a tool for flexible docking of peptides to proteins. In this article, we present a protocol for CABS-dock docking driven by information about protein-peptide contact(s). Using information on individual protein-peptide contacts allows to improve the accuracy of CABS-dock docking.
CABS-dock 是一种蛋白质-肽分子对接的计算方法，不需要预先定义结合位点。肽被视为完全灵活的，而蛋白质骨架则经历小的波动，并可选地进行大规模的重排。在这里，我们提出了一种特定的 CABS-dock 方案，该方案使用关于蛋白质-肽接触的片段信息来增强对接过程。该接触信息用于将结合肽构象的搜索缩小到结合位点的附近。我们使用单个选择和随机选择的天然蛋白质-肽接触的信息在 peptiDB 基准上验证了该方案。接触信息显著提高了 CABS-dock 的性能。该方案已作为 CABS-dock 网络服务器的新功能提供（在 http://biocomp.chem.uw.edu.pl/CABSdock/）。
CABS-dock 是一种用于肽与蛋白质的柔性对接的工具。在本文中，我们提出了一种由蛋白质-肽接触信息驱动的 CABS-dock 对接方案。使用单个蛋白质-肽接触的信息可以提高 CABS-dock 对接的准确性。
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