ChemScope

This repository contains the code used in the study Text Mining-Based Profiling of Chemical Environments in Protein–Ligand Binding Assays Across Analytical Techniques.

Data Availability

The data used in this study is available at:

• Hugging Face: ChemScope-Dataset
• GitHub: Integrated_Physicochemical_Dataset.csv

Setup

In order to run the project, you will need Python 3.8 or above. The required libraries listed in requirements.txt must be installed.

git clone https://github.com/erdemonal/ChemScope.git
cd ChemScope
pip install -r requirements.txt

Reproducing the Analysis

Fetch Resources

Download chemical property datasets from OSF (Required as data/raw is not version controlled).

python scripts/fetch_resources.py

Literature Mining

Mine Europe PMC for protein-ligand associations. Define your search queries in queries.txt (format: Name, "Search Query"). Example:

ITC, "isothermal titration calorimetry" AND ("protein-ligand binding" OR "binding affinity")

Run the miner:

python scripts/literature_mining.py

Data Processing

python scripts/data_processing.py -i data/interim -t folder

Chemometric Analysis

python scripts/chemometrics_analysis.py

Static Visualization

python scripts/static_visualization.py

Interactive Visualization

python scripts/interactive_visualization.py -i data/processed

Citation

If you use this code in your research, please cite the following paper:

Text Mining-Based Profiling of Chemical Environments in Protein–Ligand Binding Assays Across Analytical Techniques Erdem Önal, Zeynep Kalaycıoğlu
Chemometrics and Intelligent Laboratory Systems, 2026, 105659
DOI: 10.1016/j.chemolab.2026.105659

BibTeX

@article{ONAL2026105659,
title = {Text Mining-Based Profiling of Chemical Environments in Protein–Ligand Binding Assays Across Analytical Techniques},
journal = {Chemometrics and Intelligent Laboratory Systems},
pages = {105659},
year = {2026},
issn = {0169-7439},
doi = {https://doi.org/10.1016/j.chemolab.2026.105659},
url = {https://www.sciencedirect.com/science/article/pii/S0169743926000328},
author = {Erdem Önal and Zeynep Kalaycıoğlu},
keywords = {Affinity, bibliometrics, drug, visualization}