🎯 TargetX: Precision Bacterial Drug Target Identification

TargetX is an automated bioinformatics pipeline designed to rapidly screen potential drug targets from an extensive bacterial dataset. TargetX uses a systemic "negative-to-positive" filtering strategy to filter thousands of protein sequences to a handful of candidates that are essential far the survival of pathogen.

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🧬 Step-wise Workflow

TargetX doesn't just search; it eliminates. The pipeline moves through a rigorous multi-stage funnel:

1. Redundancy Reduction (CD-HIT): Collapses duplicate or highly similar sequences (90% threshold) to minimize computational overhead.
2. Host Safety Filter (Human Proteome): A negative filter to remove proteins homologous to human sequences, preventing cross-reactivity.
3. Essentiality Check (DEG): A positive filter against the Database of Essential Genes to ensure the target is critical for bacterial survival.
4. Virulence Assessment (VFDB): Identifies proteins involved in pathogenesis and toxicity.
5. Broad-Spectrum Check (ESKAPE): Filters against the most notorious multi-drug resistant pathogens.
6. Subcellular Localization (PsortB): Pinpoints the protein's location to determine accessibility for drug molecules.

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🚀 Performance Snapshot

In recent benchmarks, TargetX processed:

• Input: 10 E. coli Proteomes (~53,223 sequences).
• CD-HIT Execution: Reduced to 11,619 clusters in 40 seconds.
• Systemic BLASTing: Rapidly cross-referenced against Human, DEG, and VFDB databases.

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🛠️ Installation

TargetX requires a Linux environment with the following bioinformatics suites:

# 1. System packages
sudo apt-get update
sudo apt-get install python3-tk

# 2. Clone the repository
git clone https://github.com/cxbl-gbu/TargetX.git
cd TargetX

# 3. Create and activate the environment
conda create -n targetx python=3.10 -y
conda activate targetx

# 4. Install bioinformatics dependencies
conda install bioconda::cd-hit
conda install bioconda::blast==2.16.0

# 5. Install Python dependencies
pip install selenium

#6. Run the Tool
./dist/TargetX

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👥 Credits & Authors

TargetX was developed by CxBL (Computational and eXperimental Biomolecular Lab), Gujarat Biotechnology University (GBU).

Meet Parmar – Lead Developer

Soham Bhatt – Bioinformatics Logic & Testing

Dhaval Patel – Supervisor & Principal Investigator

Affiliation: Gujarat Biotechnology University (GBU), Gandhinagar, Gujarat, India.

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📄 License

This project is licensed under the MIT License.