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Scripts associated with the paper "Prediction of kinetics of protein folding with non-redundant contact information"
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included-proteins Aesthetic improvements May 11, 2018
.gitignore Improving description. May 11, 2018
LICENSE Initial commit Jan 16, 2018
README.md Aesthetic improvements May 11, 2018
constrn_information.py Ready for review. May 9, 2018
mypdb.pyc Initial synchronization Jan 17, 2018
proteins_17_Dec_14.csv Initial synchronization Jan 17, 2018
read-folding-rate.py Aesthetic improvements May 11, 2018
split.ods Aesthetic improvements May 11, 2018

README.md

sarw-lnkf

USAGE: python read-folding-rate.py

REQUIRES: bash utilities (ls, grep, xargs, rm, wget, gunzip) plus numpy, scipy, matplotlib

The script will create a "structures" folder under its working directory and will download over a hundred structures directly from the pdb repository. Average information will be calculated with and without redundant contacts for each structure, and bootstrapped correlations will be plotted. The entire process may take about 15-20 minutes.

Complete lists of proteins included in and excluded from the analyses will be generated automatically and written to the included_proteins.log and excluded_proteins.log files under the "included-proteins/" directory.

TODO: include source code for mypdb.py instead of compiled ".pyc" file.

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