MEGADOCK-on-Colab: an easy-to-use protein-protein docking tool on Google Colaboratory
DOI:
https://doi.org/10.51094/jxiv.374Keywords:
protein-protein docking, protein-protein interaction, MEGADOCK, Google ColaboratoryAbstract
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.
Conflicts of Interest Disclosure
none declaredDownloads *Displays the aggregated results up to the previous day.
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Submitted: 2023-05-02 16:15:49 UTC
Published: 2023-05-08 12:36:49 UTC
License
Copyright (c) 2023
Masahito Ohue
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
