MEGADOCK-on-Colab: an easy-to-use protein–protein docking tool on Google Colaboratory

[摘要] MotivationSince the advent of ColabFold, numerous software packages have been provided with Google Colaboratory-compatible ipynb files, allowing users to effortlessly test and reproduce results without the need for local installation or configuration. MEGADOCK, a protein–protein docking tool, is particularly well-suited for Google Colaboratory due to its lightweight computations and GPU acceleration capabilities. To increase accessibility and promote widespread use, it is crucial to provide a computing environment compatible with Google Colaboratory.ResultsIn this study, we report the development of a Google Colaboratory environment for running our protein–protein docking software, MEGADOCK. We provide a comprehensive ipynb file, including the compilation of MEGADOCK with the FFTW library installation on Colaboratory, the introduction of related tools using PyPI/apt, and the execution and visualization of docking structures. This streamlined environment enables users to visualize docking structures with just one click. The code is available under a CC-BY NC 4.0 license from https://github.com/ohuelab/MEGADOCK-on-Colab.

[发布日期] 2023-09-06

[关键词] Protein–protein docking;Protein–protein interaction;MEGADOCK;Google Colaboratory