Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy.
Molecules. 2022 Oct 14;27(20):6884. doi: 10.3390/molecules27206884.
Molecular docking is a key method for structure-based drug design used to predict the conformations assumed by small drug-like ligands when bound to their target. However, the evaluation of molecular docking studies can be hampered by the lack of a free and easy to use platform for the complete analysis of results obtained by the principal docking programs. To this aim, we developed PacDOCK, a freely available and user-friendly web server that comprises a collection of tools for positional distance-based and interaction-based analysis of docking results, which can be provided in several file formats. PacDOCK allows a complete analysis of molecular docking results through root mean square deviation (RMSD) calculation, molecular visualization, and cluster analysis of docked poses. The RMSD calculation compares docked structures with a reference structure, also when atoms are randomly labelled, and their conformational and positional differences can be visualised. In addition, it is possible to visualise a ligand into the target binding pocket and investigate the key receptor-ligand interactions. Moreover, PacDOCK enables the clustering of docking results by identifying a restrained number of clusters from many docked poses. We believe that PacDOCK will contribute to facilitating the analysis of docking results to improve the efficiency of computer-aided drug design.
分子对接是基于结构的药物设计的一种关键方法，用于预测小分子药物配体与靶标结合时所采取的构象。然而，由于缺乏一个免费且易于使用的平台，用于全面分析主要对接程序获得的结果，因此对分子对接研究的评估可能会受到阻碍。为此，我们开发了 PacDOCK，这是一个免费且用户友好的网络服务器，包含了用于基于位置距离和基于相互作用的对接结果分析的工具集，可提供多种文件格式。PacDOCK 通过均方根偏差（RMSD）计算、分子可视化和对接构象的聚类分析，实现了对分子对接结果的全面分析。RMSD 计算将对接结构与参考结构进行比较，即使原子被随机标记，也可以比较它们的构象和位置差异。此外，还可以将配体可视化到靶标结合口袋中，并研究关键的受体-配体相互作用。此外，PacDOCK 可以通过从许多对接构象中识别出受限数量的簇来对对接结果进行聚类。我们相信，PacDOCK 将有助于促进对接结果的分析，以提高计算机辅助药物设计的效率。
