FitDockApp: a Graphical User Interface Plugin for Template-based Docking With PyMOL
10.16476/j.pibb.2023.0307
- VernacularTitle:FitDockApp：基于模板的分子对接PyMOL插件图形化计算软件
- Author:
You-Jun WANG
1
;
Yu-Chan YANG
2
;
Yang LIU
1
;
Zhi-Xiong XIAO
1
;
Yang CAO
1
Author Information
1. College of Life Sciences, Sichuan University, Chengdu 610065, China
2. College of Computer Science, Sichuan University, Chengdu 610065, China
- Publication Type:Journal Article
- Keywords:
molecular docking;
PyMOL;
FitDock
- From:
Progress in Biochemistry and Biophysics
2024;51(3):716-725
- CountryChina
- Language:English
-
Abstract:
ObjectiveMolecular docking plays a critical role in predicting binding modes and affinity between molecules, serving as a pivotal method in structural biology and computer-aided drug design research. Our research team has recently developed a novel template-based docking method called FitDock, which outperforms commonly used molecular docking methods in terms of accuracy and speed, particularly when approximate protein-ligand templates are available. To enhance the accessibility of the FitDock method and promote its broader application in the field of molecular simulation, the development of a graphical software tool is imperative. MethodsUtilizing Python-based graphical programming, we have created FitDockApp, a plugin software for the molecular visualization software PyMOL. ResultsFitDockApp enables template-based molecular docking and ligand structure alignment through an interactive graphical interface, providing real-time visualization of predicted three-dimensional structures. It also offers the convenience of uploading docking files to a laboratory server to obtain the optimal template. Additionally, FitDockApp includes batch docking functionality. ConclusionFitDockApp simplifies the docking process through its user-friendly interface and provides robust functionality to assist researchers in obtaining precise docking results. FitDockApp is a free software compatible with both Windows and Linux systems and can be downloaded from http://cao.labshare.cn/fitdock/.
