IEEE/ACM Trans Comput Biol Bioinform. 2020 Sep-Oct;17(5):1625-1638. doi: 10.1109/TCBB.2019.2907492. Epub 2019 Mar 26.
Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the access tunnel in such a way that the ligand movement is contiguous and the energy is minimized. The result of CaverDock calculation is a ligand trajectory and an energy profile of transport process. CaverDock uses the modified docking program Autodock Vina for molecular docking and implements a parallel heuristic algorithm for searching the space of possible trajectories. Our method lies in between the geometrical approaches and molecular dynamics simulations. Contrary to the geometrical methods, it provides an evaluation of chemical forces. However, it is far less computationally demanding and easier to set up compared to molecular dynamics simulations. CaverDock will find a broad use in the fields of computational enzymology, drug design, and protein engineering. The software is available free of charge to the academic users at https://loschmidt.chemi.muni.cz/caverdock/.
在这里，我们提出了一种分析蛋白质中转运过程的新方法，称为 CaverDock。我们的方法基于改进的分子对接算法。它沿着进入隧道以连续的方式放置配体，同时最小化能量。CaverDock 计算的结果是配体轨迹和转运过程的能量分布。CaverDock 使用改进的对接程序 Autodock Vina 进行分子对接，并实现了一种用于搜索可能轨迹空间的并行启发式算法。我们的方法介于几何方法和分子动力学模拟之间。与几何方法不同，它提供了对化学力的评估。然而，与分子动力学模拟相比，它的计算需求要低得多，而且更容易设置。CaverDock 将在计算酶学、药物设计和蛋白质工程等领域得到广泛应用。该软件可在 https://loschmidt.chemi.muni.cz/caverdock/ 免费提供给学术用户使用。
