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AKT mutant allele-specific activation dictates pharmacologic sensitivities

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Instructions

Fig 3a

Heatmaps comparing the displacement of AKT1 residues in the (time-averaged) E17K and P68-77dup protein structures (Fig 3a) can be regenerated from precomputed residue-residue distance maps as follows:

Clone the github repo:

git clone https://github.com/agorelick/akt1
cd akt1

Install required R packages from CRAN:

## check for missing required packages, install them.
required.packages <- c('data.table','ggplot2','cowplot','here')
new.packages <- required.packages[!(required.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)>0) install.packages(new.packages)

Run the fig_3a.R script:

## create a PDF with figure 3a: fig_3a.pdf
Rscript fig_3a.R

Fig 3b-d

AKT1 structural diagrams in Figures 3b-d were generated using UCSF Chimera. A Chimera scene (.py format) containing an overlay of AKT1 WT and P68-77dup structures (3o96 template) is contained in this repo (data/chimera_wt_dup_overlay.py), and can be opened with UCSF Chimera to regenerate Figures 3b-d. UCSF Chimera can be freely downloaded here: https://www.cgl.ucsf.edu/chimera/download.html.

With UCSF Chimera, open the scene using: File > Open > [path-to-repo]/data/chimera_wt_dup_overlay.py. By default, only the wild-type AKT1 protein is shown (as in Fig 3b). To see the P68-77dup protein overlay, first select the P68-77dup protein: Select > Chain > A > average_dupe.pdb. Then you can show the ribbon for the P68-77dup structure: Actions > Ribbon > Show.

Citation

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  • DOI: PENDING

Contact

E-mail any questions to [email protected].