Prostruc: Protein Structure Prediction Tool

Prostruc is a command-line tool designed for comprehensive protein structure prediction, leveraging sequence alignment, template-based modeling, deep learning, and validation techniques. With a simple input of either an amino acid sequence or a FASTA file, ProStruc generates high-quality protein structures using cutting-edge algorithms. ProStruc automates the process of blast searches, template selection, structural modeling, and validation, including RMSD, TM-score, and QMEAN.

Key Features

Accepts input as a FASTA file or a raw amino acid sequence. Performs sequence alignment and template-based modeling via ProMod3 and BLAST. Incorporates deep learning-based predictions (ESMFold). Validates results using structural comparison metrics (RMSD, TM-score) and QMEAN. Supports Docker integration for handling modeling and validation engines. Outputs the top-performing models for further analysis and evaluation. Usage: You can run ProStruc from the terminal with a variety of options to customize the input and output, depending on your use case.

Basic Commands

Using a fasta file

   prostruc --fasta_file  <path_to_fasta>  --job_name <job_name>  --email <email>

Using a sequence

   prostruc --sequence <amino_acid_sequence>  --job_name <job_name>  --email <email>

Required Arguments

• --fasta_file: Path to the target protein sequence in FASTA format.
• --sequence: Input target amino acid sequence directly as a string.
• --job_name: A custom name for the prediction job.
• --email: A valid email address to receive model results.

Package Requirements

To ensure that Prostruc functions correctly, the following requirements must be met:

• Python 3.6+:
  Prostruc requires Python version 3.6 or above. Ensure that you have the appropriate Python version installed. You can check your Python version with the following command:

  python --version
  

• Docker: Docker is necessary for managing the computational workloads, including modeling and validation processes. Make sure Docker is installed and actively running in the background. Verify Docker installation and status using:

  docker --version 
  

• Internet: An active internet connection is required for Prostruc to perform BLAST searches, retrieve templates, and complete various prediction tasks.

Example

    prostruc --sequence "AAAAA" --job_name "new_protien" --email "user@example.com"