Building a Profile Hidden Markov Model for the detection of Kunitz Type Protease Inhibitor Domain

This repository contains the implementation of a computational pipeline for building a Profile Hidden Markov Model (HMM) targeting the Kunitz-type protease inhibitor domain (Pfam ID: PF00014). The Kunitz domain is a specific, highly conserved structural motif found in various proteins. This study focuses on building a developed structure-informed Hidden Markov Model (HMM) to identify Kunitz inhibitory domain in protein sequences. The profile HMM was built using high-resolution structural data from PDB The model is then evaluated on both positive (true Kunitz) and negative (non-Kunitz) protein sequences to assess its detection performance. This project was developed as part of a Laboratory of Bioinformatics during my MSc in Bioinformatics at University of Bologna.

All the process resides inside kunitz_nb folder, the notebook file with the accurate description of the entirety project pipeline is called kunitz_project_script.ipynb. Inside kunitz_nb there are all the data utilized for the project, the contents of every file is descripted inside the notebook.

The negative_kunitz.fasta (negative set downloaded from Uniprot) it's not included for its big dimension. In the notebook its described the process to recreate it by your own.