Integrating accelerated molecular simulations and AI to elucidate Cas9 specificity factors

Gayatri Panda and Arjun Ray∗

This repository contains scripts and input files used for different analysis. This Github repository contains four directories

1. spcas9-scripts 2. fncas9-scripts 3. stcas9-scripts 4. common-scripts. Files present in these folders are described pictorially. Diagram represents the structure of data storage in a GitHub repository, detailing the organization of folders and files.

All the simulation input (prmtop, inpcrd) can be accessed from the drive link:

Simulation-related files for twelve protein-complex systems (four for each Cas9 orthologs) are available in a Google Drive folder. The folder link is mentioned in the GitHub readme and provided here: https://drive.google.com/drive/u/0/folders/1QWCM3Ip4flx-d-e0MNzYq2qlxUyo7um5 The folder contains three subfolders named after the Cas9 orthologs: spcas9, fncas9, and stcas9. Additionally, there are compressed trajectory files for spcas9 and fncas9. Each ortholog folder has five subfolders:

1. Four subfolders for on-target and off-target systems containing starting structure, topology,, and coordinate file.
2. One mmgbsa subfolder containing input files used in MM-GBSA Diagram representing the structure of data storage in a Google drive folder.

Due to different input requirements for different analysis, not all files have been uploaded to this repository. Any additional files can be provided upon request.