NTxPred2 - Neurotoxic Peptide Prediction

This page serves as a comprehensive resource for users of NTxPred2, offering valuable assistance in effectively utilizing its diverse prediction modules. Within this guide, you will find detailed information, figures, and step-by-step instructions on leveraging each module integrated into NTxPred2. We aim to equip you with a clear understanding of how to navigate and make the most of every module within the platform.

GitHub & pip

🧪 Quick Start for Reproducibility

Follow these steps to replicate the core results of our paper:

# 1. Clone the repository
git clone https://github.com/raghavagps/ntxpred2.git
cd ntxpred2

# 2. Set up the environment (conda recommended)
conda env create -f environment.yml
conda activate NTxPred2

# 3. Download pre-trained models
# Visit: https://webs.iiitd.edu.in/raghava/ntxpred2/download.html
# Download the model ZIP and extract it in the root directory

# 4. Run prediction on sample input
python ntxpred2.py -i example.fasta -o output.csv -m 1 -j 1 -wd working_direcotory_path

🛠️ Installation Options

🔹 PIP Installation

To install NTxPred2 via PIP, run:

pip install ntxpred2

To check available options, type:

ntxpred2 -h

🔹 Standalone Installation

NTxPred2 is written in Python 3 and requires the following dependencies:

✅ Required Libraries

python=3.10.7
pytorch

Additional required packages:

pip install scikit-learn==1.5.2
pip install pandas==1.5.3
pip install numpy==1.25.2
pip install torch==2.1.0
pip install transformers==4.34.0
pip install joblib==1.4.2
pip install onnxruntime==1.15.1
Bio (Biopython): 1.81
tqdm: 4.64.1
torch: 2.6.0

🔹 Installation using environment.yml

Create a new Conda environment:
```
conda env create -f environment.yml
```
Activate the environment:
```
conda activate NTxPred2
```

⚠️ Important Note

Due to the large size of the model file, the model directory has been compressed and uploaded.
Download the zip file from Download Page.
Extract the file before using the code or model.

🔬 Classification

NTxPred2 classifies peptides and proteins as neurotoxic or non-neurotoxic based on their primary sequence.

🔹 Model Options

ESM2-t30 (Peptide Model): For sequences 7-50 amino acids long.
ET (Protein Model): For sequences ≥ 51 amino acids.
ET (Combined Model): For sequences of mixed length.
Default Model: ESM2-t30 (Peptide Model), selected for best performance and efficiency.

🚀 Usage

🔹 Minimum Usage

ntxpred2.py -h

To run an example:

ntxpred2.py -i example.fasta

🔹 Full Usage

usage: ntxpred2.py [-h]
                   [-i INPUT]
                   [-o OUTPUT]
                   [-t THRESHOLD]
                   [-j {1,2,3,4}]
                   [-m {1,2,3}]
                   [-d {1,2}]
                   [-wd WORKING DIRECTORY]

Required Arguments

Argument	Description
`-i INPUT`	Input: Peptide or protein sequence (FASTA format or simple format)
`-o OUTPUT`	Output file (default: `outfile.csv`)
`-t THRESHOLD`	Threshold (0-1, default: `0.5`)
`-j {1,2,3,4}`	Job type: 1-Prediction, 2-Protein Scanning, 3-Design, 4-Design all possible mutants
`-m {1,2,3}`	Model selection: 1-ESM2-t30 (Peptides), 2-ET (Proteins), 3-ET (Combined)
`-wd WORKING`	Working directory for saving results

📂 Input & Output Files

✅ Input File Format

NTxPred2 supports two formats:

FASTA Format: (Example: example.fasta)
Simple Format: (Example: example.seq, each sequence on a new line)

✅ Output File

Results are saved in CSV format.
If no output file is specified, results are stored in outfile.csv.

🔍 Jobs & Features

🔹 Job Types

Job	Description
1️⃣ Prediction	Predicts whether input peptide/protein is neurotoxic or not.
2️⃣ Protein Scanning	Identifies neurotoxic regions in a protein sequence.
3️⃣ Design	Generates mutant peptides/proteins with a single amino acid/dipeptide at a specified position.
4️⃣ Design All Possible Mutants	Generates and predicts all possible mutants.

🔹 Additional Options

Option	Description
`-p POSITION`	Position to insert mutation (1-indexed)
`-r RESIDUES`	Mutated residues (single/double letter amino acid codes)
`-w {8-20}`	Window length (Protein Scan mode only, default: 12)
`-d {1,2}`	Display: 1-Neurotoxic only, 2-All peptides (default)

📑 Package Contents

File	Description
INSTALLATION	Installation instructions
LICENSE	License information
README.md	This file
ntxpred2.py	Python program for classification
example.fasta	Example file (FASTA format)

📦 PIP Installation (Again for Reference)

pip install ntxpred2

Check options:

ntxpred2 -h

🚀 Start predicting neurotoxicity with NTxPred2!

Go to the NTxPred2 Prediction Page

Prediction Module

This module predicts neurotoxic/non-neurotoxic peptides/proteins based on the model selected by the user.

Protein Scanning

This module allows users to particularly identify neurotoxic regions within a specified protein/peptide sequence.

Design Module

This module design non-neurotoxic mutant peptides/proteins based on the user-specified residues and positions.

Important Tools

This page provides list of all the computational tools available for different types of toxicity prediction.

Download

This page allows to download the standalone and pip package of NTxPred2.

Help