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Updated: Jul 16, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
MEGADOCK-on-Colab: an easy-to-use protein-protein docking tool on Google Colaboratory
1Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-G3-56 Nagatsutacho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan. ohue@c.titech.ac.jp.
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 .
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