NTxPred2

A method for predicting the neurotoxic activity of peptides and proteins.

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📌 Introduction

NTxPred2 is designed to assist researchers in therapeutic peptide and protein development by providing advanced methods for quantifying and classifying neurotoxic peptides and proteins that target the central nervous system.

It employs large language model word embeddings as features for predicting neurotoxic activity. The final model offers Prediction, Protein-Scanning, and Design modules, implemented using machine learning and protein language models.

🔗 Visit the web server for more information: NTxPred2 Web Server

📖 Please cite relevant content for complete details, including the algorithm behind the approach.

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📚 Reference

Rathore et al. A large language model for predicting neurotoxic peptides and neurotoxins. #Journal Name#

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🖼️ NTxPred2 Workflow Representation

🛠️ Installation

🔹 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

1. Create a new Conda environment:

conda env create -f environment.yml

2. Activate the environment:

conda activate NTxPred2

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⚠️ 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.

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🔬 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.

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🚀 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

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📂 Input & Output Files

✅ Input File Format

NTxPred2 supports two formats:

1. FASTA Format: (Example: example.fasta)
2. 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.

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🔍 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)

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📑 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)
example.seq	Example file (Simple format)

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📦 PIP Installation (Again for Reference)

pip install ntxpred2

Check options:

ntxpred2 -h

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🚀 Start predicting neurotoxicity with NTxPred2 today!

🔗 Visit: NTxPred2 Web Server