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- Title
MEGADOCK-on-Colab: an easy-to-use protein–protein docking tool on Google Colaboratory.
- Authors
Ohue, Masahito
- Abstract
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. The code is available under a CC-BY NC 4.0 license from https://github.com/ohuelab/MEGADOCK-on-Colab.
- Subjects
INTEGRATED software; PROTEIN-protein interactions
- Publication
BMC Research Notes, 2023, Vol 16, Issue 1, p1
- ISSN
1756-0500
- Publication type
Article
- DOI
10.1186/s13104-023-06505-w