🎬Follow-Along Platform Tour

Follow the steps shown in this video to upload your first files, create your first workspace with an AI pipeline, then turn it into a point and click tool with Ontologic.

How to use this Tutorial

First, sign up for your Ontologic trial or individual account with the link provided to you. Then you can watch this video and follow along!

Look out for the indicated time jumps where you'll have to wait for your code to run or workspace to save.

We've also included downloadable or copyable code and files for every step of the video, below.

Data

For uploading:

585B

affinity.yaml

Boltz-2 GitHub link for background:

Not found

Workspaces Code for Copying

To update dependencies and install Boltz-2:

sudo apt update
sudp apt install python3-pip
pip install boltz[cuda] -U

Contents of affinity.yaml input file:

version: 1  # Optional, defaults to 1
sequences:
  - protein:
      id: A
      sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
      msa: empty
  - ligand:
      id: B
      smiles: 'N[C@@H](Cc1ccc(O)cc1)C(=O)O'
properties:
  - affinity:
      binder: B

To run the Boltz-2 affinity prediction:

boltz predict files/affinity.yaml --out_dir ./results --num_workers 0

Note that your path may be different depending on the location of your input file! If your file is not in a folder in the workspace, simply enter "affinity.yaml", and if you've uploaded into the Project Data folder, enter "projectData/affinity.yaml"

Tools Code for Copying

Command to set the tool:

boltz predict affinity.yaml \
   --num_workers 0 \
   --output_format pdb \
   --out_dir ./outputs 

Make sure to select the entire input file path when you're replacing it with a parameter! For the code block above, this is just "affinity.yaml". If your path was something like "projectData/affinity.yaml", make sure to select the whole phrase, including the parent folder(s), as the item to replace with a parameter