BEPT stands for Beginner friendly Electrostatics for Protein analysis Tool, is a command line tool, developed by IISc-Software Team, participating in iGEM 2024.

This blog is about why bept was made, its features how it helps the community for doing protein electrostatics. Official Github Repository at: https://github.com/IISc-Software-iGEM/bept

Features of Bept

Ever wished protein electrostatics could be as easy as just typing protein file names and choosing options? That's where BEPT comes in! It is designed to make your life easier, BEPT lets you perform electrostatics calculations without the steep learning curve. Let's take a quick tour of what makes BEPT truly special:

• Interactive Commands, No Hassle: Need to generate pdb2pqr or APBS .in files? BEPT walks you through it interactively—no more hunting through dense documentation.

• Comprehensive Outputs: Get everything you need in one go—PQR files, potential DX maps, and even our exclusive .bept file, packed with all the key protein details.

• Automation & Flexibility: Easily automate PDB2PQR and APBS runs, or switch to interactive mode if you prefer more control. It's your choice!

• Surface Residue Data & SASA: BEPT doesn’t stop at electrostatics. It also calculates surface residues and Solvent Accessible Surface Area (SASA) values for deeper insights.

• Pre-made PyMOL Templates: Skip the coding hassle! We’ve got pre-made PyMOL Python templates ready for you to use, speeding up visualization.

• Smart Caching & History: Save your .in files for later or check your command history. No need to re-create commands you've already run—BEPT remembers for you.

• User-Friendly UI: Worried about complicated command syntax? Don’t be! BEPT’s friendly UI guides you every step of the way.

• Read the Docs, On-the-Go: Access our interactive documentation straight from the command line. No browser needed!

• Colorful, Easy-to-Read Outputs: With clear color coding and smart error handling, BEPT ensures that working with protein electrostatics feels intuitive and stress-free.

Who is Bept for?

Bept is designed for anyone interested in studying protein electrostatics, especially APBS Electrostatics. It caters to a wide audience, including students, research professionals, and industrialists. The intuitive and interactive interface makes it accessible to all, regardless of their prior experience with command-line tools. No need to be scared of long and hard command line tool documentation.

With Bept, users can confidently pursue research in protein electrostatics, contributing to faster scientific development and discovery globally.

How to use bept?

You can know all about how to use Bept anywhere, from online to right in your terminal. Bept provides are very intuitive documentation along with easy to read offline docs. View the documentation -

• Offline by simply running bept docs.

• Online at ReadTheDocs.

If you are unfamiliar with using command line tools, don’t worry, Bept also provides a very simple UI to produce bept commands to run. Simply run bept ui and you get a simple intuitive interface where you just input your data files, choose options and you are good to go!

Why just bept?

You might also be wondering, there are so many pre-existing libraries and tools, web-servers and more for protein electrostatics. Why should I choose BEPT?

Well as a part of the scientific community, our main goal is to push forward the research in biological sciences. Thus, it doesn’t matter which tool you use, as long as you know what you are doing and how to use it. For beginners, currently existing tools might be a bit overkill to directly use and understand their usages.

You might notice bept doesn't provide anything “new” that the world already has when it comes to protein electrostatics since it uses pre-existing material only. But the point is the bept dumbs it down and makes it very beginner-friendly, just run a single command it does everything for you. In Gen-Z slang, you could say, Bept doesn’t let your skill issue show up, while letting your rizz flow in instants.

Creating Bept

Bept is created by IISc-Software Team, participating in iGEM 2024 along with few future iGEMers of IISc, Bengaluru. It was lead by Anirudh Gupta(the blog writer). All acknowledgements are mentioned in the Official Github repository.

Summary

BEPT, or Beginner friendly Electrostatics for Protein analysis Tool, is a command line tool developed by the IISc-Software Team for iGEM 2024 to simplify protein electrostatics calculations. It offers interactive commands, comprehensive outputs, automation, and user-friendly features for students, researchers, and industrialists. BEPT aids in generating electrostatic data, calculating surface residues, visualizing through PyMOL templates, and provides on-the-go documentation. While not offering new methodologies, it streamlines existing processes to be beginner-friendly and accessible, fostering scientific research and discovery.