Highly charged protein regions have secondary structure and conserved sequence properties

Layout

code

• analysis: Jupyter notebooks used to analyze and visualize raw data.
• processing: Jupyter notebooks used to filter or extract subsets of raw data.
• scripts: Python scripts containing functions used to perform analysis in analysis and processing.
• tests: All test suites for code in scripts.

data

• af_regions: Protein regions extracted from the AlphaFold dataset.
• charged_regions: List of charged regions. cr_raw.csv contains the raw output from extract_charged_regions.py. cr_filtered*.csv contains the list of charged regions with a verified orf and a valid AYbRAH MSA. cr_filtered_aflabel.csv has an appended column characterizing the structure of the region based on AlphaFold prediction. cr_filtered_lrlabel.csv has an appended column characterizing the structure of the region based on prediction by the logistic regression model. cr_filtered_unlabeled.csv contains the list of regions whose structure cannot be defined based on the AlphaFold prediction.
• misc: All other data files used.
• ref_proteomes: Reference proteomes from SGD and 1000 Fungal Genomes Project.
• sc_orfs: List of Sacharomyces cerevisae ORFs with different attributes.
• uversky: Output files from Uversky analysis.

figures

Jupyter notebooks used to produce final figures for the manuscript.

misc

Notes and color schemes.