# Oncogenic mutations in the DNA-binding domain of FOXO1 disrupt folding: quantitative insights from experiments and molecular simulations
### This data repository includes all trajectory data and log files to perform the analyses outlined in https://doi.org/10.1021/acs.biochem.2c00224. This repository is in accessory to the [Git Repository](https://github.com/vvoelz/FOXO1-folding/tree/master/Paper_scripts) for this publication.
#### Contents:
* MSM Files
* These files are necessary in companion to scripts and files in the Git repository to reproduce MSM analysis outlined in the manuscript.
* **distances_tica2.5_output.npy**
* **distances_cluster_1000_4_centers.npy**
* **distances_cluster_1000_4_dtrajs.npy**
* **distances_msm_10_100**
* CKTest
* This component contains file necessary to perform CKTest. Companion script in Git repository
* **cktest.h5**
* Google Drive
*This component contains all trajectory and structural data for FEP simulations and MSM simulations in manuscript.
* FOXO1.gro : Structure file for MSM trajectories.
* FOX01_trajs_tar.gz (contact Dylan Novack: tuj66686@temple.edu)
* Contains directories **RUN0..RUN19**, each containing *.xtc* trajectories for folding@home simulations starting from the corresponding structure.
* FOXO1_FEP_data.tar.gz (contact Lei Qian: leiqian-temple2@outlook.com; or tuk04130@temple.edu)
* TRIPEP_FEP_deposit:
* Contains **eight directories** ( *L183P, S205T, T182M, A166V, A166G, S153R, S152R, L183R*) with **30 sub-directories** for 30 λ indices, and an **MDP** directory containing gromacs mdp files.
* Each λ directory contains **eight sub-directories** for each FEP simulation stage: *EM, NVT, NPT, Production_MD(0-1ns), Production_MD_II (1-2ns), Production_MD_III (2-4ns), Production_MD_IV (4-6ns), Production_MD_V (6-8ns)*. The structure files (gro files) can be found in each of these eight sub-directories. Production runs of each model were performed for **8 ns in the NPT ensemble**. For each simulation performed using a given value λi, the values of ∂U/∂λ and ΔUij = U(λj) – U(λi) were written to file every **0.5 ps**, for all intermediates j. For the trajectory timestep, it is the same as lambda timestep **0.5 ps**.
* FOXO1_FEP_deposit
* Same directory layout as TRIPEP_FEP_deposit
* FOXO1_INTERM_FEP_deposit
* **Six directories** for six folding intermedates of FOXO1 FKH domain: *CC235, CC520, CC396, CC372, CC765, CC779*. Same directory layouts as previous two repositories.
