1H-CEST

Fitting scripts for 1H CEST data

Ref: Liu et al, (2021) "Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino 1H CEST" Magnetic Resonance

csv_output: the folder contains fitting results for 1HCEST data assuming no exchange

csv_output_no_kex: the folder contains fitting results for 1HCEST data assuming there is exchange

inside csv_output or csv_output_no_kex, result1-9.csv are the 1HCEST raw data for all 9 peaks in the 1D imino spectra;

Fit_1-9 are the folders contains all the fitting results;

batch_CEST_fit.py or batch_CEST_fit_offset_filter.py are the fitting scripts to fit 9 1HCEST profiles, with or without constraining offsets

inside each fit folder (e.g. Fit_1), cest_fit_final_v10.py is the 1HCEST fitting script and BMNS_params_v10.txt is the input parameters for fitting, test is the folder including fitting results

The plot_profile.py script is used to plot the 1HCEST data without fitting. To plot the result_1.csv data, use the command "plot_profile.py result_1.csv"

python 2.7 is required for the scripts described above

residual_AIC_BIC_HCEST_v2.py (python 3.6 needed for this script), this scirpt is used to combine all fitting results (profiles in pdf and exchange parameters in csv)

the csv_output and csv_output_no_kex folders are the input, the assignment should be changed in line 246 in residual_AIC_BIC_HCEST_v2.py

the output files are

1. *_fit.pdf, which is the pdf containing all 1HCEST profiles assuming there is exchange;

2. *_nokex.pdf, the pdf containing all 1HCEST profiles assuming no exchange

3. *_combined.pdf, the combination of 1 and 2

4. *_fitparm.csv inside csv_output, the fitting parameters for all 9 1HCEST fitting

5. residual_*_residual.pdf, the residual plot and AIC/BIC values for each 1HCEST profile

The folder hcest_run_v2 contains the most updated 1HCEST fitting/analysis scripts

In this workflow, the fitting is performed on the Duke computer cluster

the detailed protocol is provided in the README file inside the hcest_run_v2 folder