GSOC’25 Project: Improving New Drug Modality Support

Sonalilipsa17375 · May 16, 2025, 5:57pm

Hello DeepChem Community ,

I’m Sonali Lipsa Patra, a 3rd yr. UG student in the EE department at NIT Rourkela, Odisha, India. I am excited to share that I will be working on the project Improving New Drug Modality Support for Antibody Drug Conjugates (ADCs) this summer as part of GSoC’25.

Throughout the project, I will be sharing weekly updates on my progress here. I am looking forward to engaging with the community and welcome feedback and suggestions from all.

Looking forward to learning, contributing, and having great discussions. Stay tuned for more updates.

Regards,
Sonali Lipsa Patra

NTHamda · May 20, 2025, 11:59am

Congratulations, wishing you a rewarding and impactful GSoC’25 journey ahead. Looking forward to seeing your project!

Sonalilipsa17375 · June 10, 2025, 5:43am

Week-1 Updates :

Explored the ADC Payload Bioactivity Dataset from ChEMBL to analyze the distribution of IC50 values for DNA topoisomerase I, a key target for ADC payloads. Link to Dataset
Studied the DeepChem documentation on adding new datasets to MoleculeNet. Link
Created a draft PR covering the introduction to ADCs and the overview of basic sciences. Draft PR
Addressed previous review comments on ADC-related literature in the tutorial and will continue upgrading the section in phases.

Link to Slides Deck

Sonalilipsa17375 · June 13, 2025, 5:12pm

Week-2 Updates :

Continued exploring the ChEMBL dataset for DNA topoisomerase I inhibitors, key for ADC payload identification. [Link to ChemBL dataset]
Studied this amazing paper on ADC payload activity prediction. [Link]
Uploaded the ChEMBL dataset to a personal AWS account, and preparing for Molecule Net integration.
Visualized IC50 distribution with a log-scale histogram to assess compound potency. [Link to Notebook].
Physicochemical Property Analysis: Analyzed IC50 value distribution. Planned visualizations for Molecular Weight and AlogP to study conjugation and delivery properties.
Refined the ADC tutorial draft PR, addressing feedback on literature and incorporating script insights. [Link to Draft PR].

Link to Slides deck : https://docs.google.com/presentation/d/1GRsTgPoTBwrouery58OWFU7mrRUsvGaLdysTS_lebsA/edit?usp=sharing

Sonalilipsa17375 · June 20, 2025, 4:25pm

Week-3 Updates:

Added the Approved ADCs dataset into the assets, (as the approved ADCs data is low, 22 approved ADCs, so added under assets).
Created both 2D and 3D renderings of an example ADC (Brentuximab vedotin) payload to illustrate structural features.
Standardized IC₅₀ values and generated a binary active/inactive label based on potency thresholds.
Implemented code to visualize key payload properties - IC₅₀ (nM), and AlogP against the DNA Topoisomerase‑1 .
[ Link to PR ] - https://github.com/deepchem/deepchem/pull/4441
[Link to slides deck] :
https://docs.google.com/presentation/d/1GRsTgPoTBwrouery58OWFU7mrRUsvGaLdysTS_lebsA/edit?usp=sharing