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AlphaCryo4D v0.1.1 Development Version

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AlphaCryo4D is an open-source free software released under GNU General Public LICENSE that implements 3D classification of single-particle cryo-EM data using deep manifold learning and novel energy-based particle voting methods (originally proposed in the following publication). AlphaCryo4D v0.1.1 is currently a development version, NOT a stable released version. The authors are currently optimizing the code architecture and adding novel features to the system. The future version of this open-source software will be updated with a user-friendly interface. Users are free to use and modify the source code, providing their compliance with the GPL and that any publication making use of this software shall cite the following publication:

Reference:

Zhaolong Wu, Enbo Chen, Shuwen Zhang, Yinping Ma, Youdong Mao. Visualizing conformational space of functional biomolecular complexes by deep manifold learning. Int. J. Mol. Sci. 23(16), 8872 (2022). https://doi.org/10.3390/ijms23168872

References of potentially used software:

EMAN2: Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees, I., & Ludtke, S. J. EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol, 157(1), 38-46 (2007). doi:10.1016/j.jsb.2006.05.009

RELION: Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol, 180(3), 519-530 (2012). doi:10.1016/j.jsb.2012.09.006

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Installation:

It is recommended to install EMAN2 and RELION before using AlphaCryo4D according to the websites https://github.com/cryoem/eman2 and https://github.com/3dem/relion respectively.

1. Download the source code:

git clone https://github.com/AlphaCryo4D/AlphaCryo4D.git

cd AlphaCryo4D/

2. Create the conda environment:

conda create -n AlphaCryo4D python=3.7.1

3. Activate the environment:

source activate AlphaCryo4D

4. Install the dependencies:

conda install --yes --file EnvConda.txt

pip install -r EnvPip.txt

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Documentation:

Programs and scripts are described in Docs/documentation_alphacryo4d.pdf. An example tutorial is provied in Docs/tutorial_alphacryo4d.pdf. The procedures are tested on the operating system of CentOS Linux release 7.6.1810. Please do not hesitate to reach our team should you encounter issues in using this system.

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The AlphaCryo4D Development Team:

Youdong Mao (PI), Zhaolong Wu, Shuwen Zhang, Yinping Ma, Wei Li Wang, Deyao Yin. (May 2022).

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Copyright ©2022 | The AlphaCryo4D Development Team