CD Spectroscopy Heatmaps

Input Files

Local directory must contain CSV files where:

• Row names are partial sequences TTAXXX (e.g. TTAGGG → GGG)
• Column names are ligand concentrations (μM)
• Contents are relative structural stabilities

Generation

In cd_spectra_heatmap.ipynb, navigate to the following cell:

FILENAME = 'CHANGE'
TITLE = 'LIGAND, CATION'

Change these values such that:

• FILENAME = Input CSV filename
• TITLE = Heatmap title Finally, run the notebook. Generated image will be saved as the file {FILENAME}.png.

Docking Score Jitterplots

Input Files

Local directory must contain CSV-formatted text files with name format dock_{CONF}_{STRUCT}_{sequence}_100_50poses.txt

• CONF: G-quadruplex conformation (parallel, antiparallel, hybrid)
• STRUCT: Structure ID
• Sequence: Partial sequence TTAXXX (e.g. TTAGGG → GGG)

Binding affinities (kcal/mol) must be included under the heading S

Generation

In docking_jitterplots.ipynb, navigate to the following cell:

LIG = 'CHANGE'
CONF = 'CHANGE'
STRUCT = 'CHANGE'

Change these values such that:

• LIG = Ligand docked
• CONF = G-quadruplex conformation (parallel, antiparallel, hybrid)
• STRUCT: Structure ID

Finally, run the notebook. Generated image will be saved as the file {LIG}_{STRUCT}_{CONF}.png.