Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA.
Nat Protoc. 2013;8(7):1277-98. doi: 10.1038/nprot.2013.074. Epub 2013 Jun 6.
Structure-based drug design is frequently used to accelerate the development of small-molecule therapeutics. Although substantial progress has been made in X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, the availability of high-resolution structures is limited owing to the frequent inability to crystallize or obtain sufficient NMR restraints for large or flexible proteins. Computational methods can be used to both predict unknown protein structures and model ligand interactions when experimental data are unavailable. This paper describes a comprehensive and detailed protocol using the Rosetta modeling suite to dock small-molecule ligands into comparative models. In the protocol presented here, we review the comparative modeling process, including sequence alignment, threading and loop building. Next, we cover docking a small-molecule ligand into the protein comparative model. In addition, we discuss criteria that can improve ligand docking into comparative models. Finally, and importantly, we present a strategy for assessing model quality. The entire protocol is presented on a single example selected solely for didactic purposes. The results are therefore not representative and do not replace benchmarks published elsewhere. We also provide an additional tutorial so that the user can gain hands-on experience in using Rosetta. The protocol should take 5-7 h, with additional time allocated for computer generation of models.
基于结构的药物设计常用于加速小分子治疗药物的研发。尽管在 X 射线晶体学和核磁共振（NMR）光谱学方面取得了重大进展，但由于频繁无法结晶或获得大量或灵活蛋白质的足够 NMR 约束，高分辨率结构的可用性有限。当没有实验数据时，计算方法可用于预测未知蛋白质结构和建模配体相互作用。本文描述了一个使用 Rosetta 建模套件将小分子配体对接入比较模型的综合而详细的方案。在本文提出的方案中，我们回顾了比较建模过程，包括序列比对、穿线和环构建。接下来，我们介绍将小分子配体对接入蛋白质比较模型。此外，我们讨论了可以改善配体对接入比较模型的标准。最后，也是很重要的一点，我们提出了评估模型质量的策略。整个方案仅以一个示例呈现，该示例完全是出于教学目的选择的。因此，结果不具代表性，不能替代其他地方发表的基准。我们还提供了一个额外的教程，以便用户在使用 Rosetta 时获得实践经验。该方案大约需要 5-7 小时，外加计算机生成模型的时间。
