Metal Binding Sites Deep Learning
This repo contains the code to run the physiological-adventitious MBS classifier. The outcome of the classifier is a csv file containing the predictions for each MBS given as input.
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For each site, create a dictionary containing the features as described in the paper and save it as pickle file. Zinc and iron sites used in this work are available as examples.
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Create a folder containing the MBS data as described in the paper.
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Create a csv file with header ['site', 'length'] containg the names of the files and their lengths.
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Run the following command
python Classify.py --data_path <data_to_test_folder> --list_path <data_to_test_folder/mbs_list.csv>
- create two empty folder 'zinc' and 'iron'
- download and extract the MBS data in the respective folders.
Link to data
To classify zinc data:
python ClassifyAllSites.py --metal zinc
To classify iron data:
python ClassifyAllSites.py --metal iron