🚀 New Release: ProteinPrep – A Lightweight Tool for Protein  Prep.

Date: August 22, 2025

The Insilico Lab is excited to announce the release of ProteinPrep, a new lightweight yet powerful tool designed to streamline protein structure preparation for docking and related computational workflows.

Protein preparation is a critical first step in computational chemistry, chemoinformatics, bioinformatics, and computer-aided drug design (CADD). Traditionally, this process requires multiple tools and manual intervention — downloading protein structures, cleaning them, removing unnecessary components, and generating docking-ready formats. ProteinPrep simplifies this entire workflow into a single, user-friendly package.

🔬 Key Features of ProteinPrep

• Automatic PDB Fetching: Retrieve protein structures directly from the RCSB database with built-in retry logic.

• Structure Cleaning: Remove water molecules and heteroatoms, while retaining specific chains or ligands when needed.

• Docking-Ready Conversion: Add hydrogens (protonation) and convert to PDBQT format using OpenBabel.

• Flexible Interfaces: Choose between a command-line interface (CLI) for automation or a graphical user interface (GUI) for accessibility.

• Colab Integration: Run directly on Google Colab, making it accessible without local installation.

• Detailed Reporting: Automatically generates JSON logs summarizing all operations performed.

🌍 Why It Matters

For researchers in drug discovery, structural biology, molecular docking, and virtual screening, protein preparation can be time-consuming and error-prone. ProteinPrep offers a compact yet versatile solution that bridges the gap between accessibility and computational rigor, making it easier for both beginners and experienced researchers to prepare high-quality protein inputs.

📂 Availability

ProteinPrep is now available on GitHub, complete with documentation, installation instructions, and usage examples.
🔗 GitHub Repository Link

💬 Call for Feedback

This is the first release, and we welcome feedback from the community to refine and expand its features. Whether you are a computational chemist, bioinformatician, or part of a CADD team, your insights will help shape the next iteration of ProteinPrep.