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

Ohue, Masahito

doi:10.51094/jxiv.374

##article.authors##

Ohue, Masahito School of Computing, Tokyo Institute of Technology https://orcid.org/0000-0002-0120-1643

DOI:

https://doi.org/10.51094/jxiv.374

キーワード:

protein-protein docking、 protein-protein interaction、 MEGADOCK、 Google Colaboratory

抄録

Motivation: Since 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.

Results: In 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.

Availability: The code is available under a CC-BY NC 4.0 license from https://github.com/ohuelab/MEGADOCK-on-Colab.

利益相反に関する開示

none declared

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ダウンロード実績データは、公開の翌日以降に作成されます。

引用文献

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