Drug Target Selection and Validation Pipeline

Greetings Fellow Developers!

I’m Anamika and 'm thrilled to be part of GSOC 2024, contributing to DeepChem. I’ll be working on introducing drug target selection and validation pipeline in deepchem. I’ll integrate ConPLex for target selection and ESM for target validation into DeepChem, addressing the need for target selection and validation pipeline in DeepChem. By enhancing DeepChem with these capabilities, my project aims to streamline the drug discovery process, offering high accuracy in drug-target interaction predictions and insightful structural and functional analyses of potential targets.

This forum thread serves as a hub to monitor the progress of this project.

Thank you for your interest! Drop by occasionally for updates!

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Week 1 Update:

  • Studied basic science behind the drug target selection and validation
  • Looked into how Open Target works
  • Updated the tutorial to reflect the basic science of target selection and validation
  • Build a dataset of top proteins and drug molecules to test the pipeline

Tutorial on target selection and validation :https://colab.research.google.com/drive/14xdoLXRMI7Kg_g8lpAmKkwurdB432jFT#scrollTo=axXgO2x81OP8 . My ongoing attempt to train the model: https://colab.research.google.com/drive/1AP_KXtSmczN5NeJtb0tO2Gno27A5Zlt5#scrollTo=UYyF7NT8gq2Z

Progress report Week 2:

I dived in deeper to understand the key concept of the drug target selection. I woked on implementing a Drug Target Interaction model I had porposed in the GSoC proposal. It can be found in the last section of this colab notebook: https://colab.research.google.com/drive/14xdoLXRMI7Kg_g8lpAmKkwurdB432jFT#scrollTo=tJLc3zrrZ4qg . The Drug Target Interaction tutorial is incomplete and I’ll revisit it later in the gsoc period to comlete it and merge in DeepChem.

Progress Report Week 3 and 4:

  • I tested my DTI model from previous week on the protein dataset that I build in 1st week.
  • Then moved on preparing a tutorial on basic science of Target Selection and Validation.
  • Got it reviewed by Dhuvi and Elisa.
  • Based on the reviews decided to split the tutorials in 5 parts:
  1. Protein structure prediction
  2. Druggability assesment
  3. Functional Domain Prediction of target protein
  4. Drug target interaction
  5. Target selection
  • Started Working on 1st part of the tutorial which is protein structure prediction with ESMfold.

Progress report week 5:

  • Raised the PR for Protein structure Prediction with ESMFold.
  • Started worked on drugability tutorial.

Progess report week 6:

  • I was unavailable for work
  • Got PR reviewed

Progress report week 7:

  • I got my protein Structure prediction tutorial merged in.

  • I started working on Druggability tutorial which has 2 parts : the 1st part is basic explanation of druggability and its relevance in target selection. The 2nd part is application of Fpocket and ML model to identify the pockets and classify them into druggable and undruggable.

  • I was stuck with finding a right dataset for training my model.