dmbala / ai4fold_tutorials

AI4Fold_Tutorials

Initial Setups

Compute Accounts

• Register for the Robetta server account https://robetta.bakerlab.org/register.php (takes about a minute)
• For using colab, you need an active gmail account https://support.google.com/mail/answer/56256?hl=en (takes about a minute)
• Rutger's participants with an active Rutger's netid can apply for the Amarel cluster account: https://oarc.rutgers.edu/amarel-cluster-access-request/

SSH clients

* Chrome Browser - Secured Shell App: https://chrome.google.com/webstore/detail/secure-shell-app/pnhechapfaindjhompbnflcldabbghjo?hl=en
* Windows OS - git bash: https://gitforwindows.org/
* Others: puTTY, moabaxterm, winscp,

Main Folders

AF2 (AlphaFold2 examples - running with full db, reduced db, and msa+structure prediction)
AnalysisScripts (scripts to get RMSD and pTM plots)
RF (RoseTTAFold examples)

How to get structure of a protein from its sequence.

• Query PDB
• Query AlphaFoldDB
• Do prediction on
  • AF2 or RoseTTAFold servers
  • local cluster/workstation or external resources like XSEDE, National Supercomputers, Cloud

Pointers to external Resources

• Query PDB: https://www.rcsb.org/
• Query AlphaFoldDB https://alphafold.ebi.ac.uk/
• Robetta Server: https://robetta.bakerlab.org/
• AlphaFold Colab: https://colab.sandbox.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb

Local Clusters/Workstation

Conda
Docker/Singularity

Submitting jobs to the cluster via SLURM

SSH into the cluster. For this step, you need to open a terminal, SSH client, or web access method like Open Ondemand, Chrome Shell App, or Fastx.

ssh <netid>@amarel.hpc.rutgers.edu

Clone this repository

>  git clone https://github.com/dmbala/AI4Fold_Tutorials

(On Amarel cluster, try "cp -r /projects/oarc/users/training/AI4Fold AI4Fold_Tutorial")

>  cd AI4Fold_Tutrials

To run all the jobs

> ./run_all_jobs.sh

Now check your jobs:

> squeue -u <netid> 

Note that if you are not running this on the Amarel clsuter, please modify the db and bin path in the wrapper scripts, and change the patition names and other parameters specific to your local cluster.

Slides

https://drive.google.com/file/d/1AfIXfBuxTPMuU3v9M2XJjx2DxBXUaGAI/view?usp=sharing