Dataset Information

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

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 .

SUBMITTER: Ohue M

PROVIDER: S-EPMC10515421 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Publications

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

Ohue Masahito M

BMC research notes 20230922 1

<h4>Motivation</h4>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 pro ...[more]

PMID: 37737185

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Dataset Information

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

Motivation

Results

Publications

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

Similar Datasets

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