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

BMC Research Notes

Research Note

Masahito Ohue¹ 

[1] Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-G3-56 Nagatsutacho, Midori-ku, 226-8501, Yokohama, Kanagawa, Japan;

关键词: Protein–protein docking;    Protein–protein interaction;    MEGADOCK;    Google Colaboratory;   

DOI  :  10.1186/s13104-023-06505-w

 received in 2023-05-11, accepted in 2023-09-06,  发布年份 2023

来源: Springer

【 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.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

【 图 表 】

Fig. 1