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computational-chemical-biology / ChemWalker

BSD 3-Clause "New" or "Revised" License
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ChemWalker

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ChemWalker is a python package to propagate spectral library match identities through candidate structures provided by in silico fragmentation, using random walk.

Installation

Install conda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Create a dedicated conda environment and activate

conda env create -f environment.yml
conda activate chemwalker 
pip install git+https://github.com/computational-chemical-biology/ChemWalker.git

Third party

ChemWalker was tested on MetFrag2.3.-CL.jar, download MetFrag CL here. Old releases can be found here.

References

Tiago Cabral Borelli, Gabriel Santos Arini, Luís G P Feitosa, Pieter C Dorrestein, Norberto Peporine Lopes, Ricardo R da Silva. Improving annotation propagation on molecular networks through random walks: introducing ChemWalker. Bioinformatics 2023, 39(3), btad078.

ChemWalker uses MetFrag for in silico annotation Wolf, S.; Schmidt, S.; Müller-Hannemann, M.; Neumann, S. In Silico Fragmentation for Computer Assisted Identification of Metabolite Mass Spectra. BMC Bioinformatics 2010, 11 (1), 148.

ChemWalker uses the Fusion concept, proposed on MetFusion, for ranking improvement from spectral library. Gerlich, M.; Neumann, S. MetFusion: Integration of Compound Identification Strategies. J. Mass Spectrom. 2013, 48 (3), 291–298.

License

This project is licensed under the BSD 3-Clause License - see the LICENSE file for details