VSpipe-GUI
Python · Bash · Molecular Docking
Interactive graphical interface for virtual screening and hit selection, running on Windows, Mac, and Linux. Covers receptor preparation, compound library prep, virtual screening, results visualization and filtering. Published in Int. J. Mol. Sci. (2025).
VSpipe-Agent
Python · ADK · AI Agents · Virtual Screening
AI agent built with Google's Agent Development Kit (ADK) for structure-based virtual screening — implements real Lipinski filtering and AutoDock Vina docking, adapted from VSpipe-GUI. Developed as a Kaggle 5-Day AI Agents capstone (Agents for Good).
VeSpA
Python · Computational Pathology · IMC
Vessel Spatial Analysis toolkit for imaging mass cytometry (IMC) data — developed at the Computational Pathology Lab, Humanitas Research Hospital, for spatial analysis of the tumor vasculature.
View Repository
imc-nextflow-pipeline
Nextflow · IMC · Reproducible Pipelines
Nextflow pipeline for automated, reproducible processing of imaging mass cytometry (IMC) data, from raw acquisition through to analysis-ready outputs. Built at the Computational Pathology Lab, Humanitas Research Hospital.
View Repository
Complete IMC Analysis Workflow
Python · IMC · Single-Cell Analysis
End-to-end workflow for imaging mass cytometry analysis — covering segmentation, cell phenotyping, and spatial statistics for multiplexed tissue imaging. Developed at the Computational Pathology Lab, Humanitas Research Hospital.
View Repository
BioPredict
Python · Machine Learning · Streamlit
ML-based QSAR web application predicting bioactivity against Receptor Tyrosine Kinase using ChEMBL data. Built with Scikit-learn, RDKit fingerprints, and Streamlit for interactive deployment. Co-developed with Yasir Waheed.
MD Simulator
Python · GROMACS · GUI
Python-based graphical interface for macromolecular simulations on GROMACS — automates preparation, solvation, ionization, energy minimization, and full MD simulation runs. Co-developed with Yasir Waheed.
SPECTRUM
MATLAB · Proteomics
A comprehensive MATLAB toolbox for proteoform identification from top-down proteomics data — statistical profiling, peptide analysis, and visualization. Published in Scientific Reports (Nature, 2019).
COVID-19 Bioactivity Predictor
Python · QSAR · Streamlit
QSAR model and Streamlit web application for predicting inhibitor potency against SARS-CoV-2 Replicase Polyprotein. Uses PubChem fingerprints and Random Forest for end-to-end bioactivity (pIC50) prediction.
PyMOL Script Repository
Python · PyMOL · Structural Biology
Collection of PyMOL scripts for structural analysis, visualisation, and automation — covering protein structure inspection, binding site analysis, and publication-quality molecular rendering.
