About juProt
juProt (https://juprot.info/) is an open-source web application designed to facilitate the rapid and user-friendly comparative analysis of protein-ligand interaction networks, with an initial focus on hydrogen bonds. Understanding how ligands interact with their protein targets, and how these interactions change due to mutations or when comparing different ligands, is fundamental in structural biology, bioinformatics, and drug discovery.
Motivation
While powerful tools exist for analyzing interactions in a single protein-ligand complex, comparing these interactions across two different complexes often requires manual data extraction, scripting, and collation of results. juProt aims to simplify this process, making comparative interaction analysis accessible to a broader range of researchers and students without requiring extensive computational expertise.
Core Technology
juProt is developed using the Julia programming language, leveraging the high-performance Genie.jl web framework for its backend and user interface. The core interaction detection is powered by the well-established Protein-Ligand Interaction Profiler (PLIP), a Python-based tool. juProt interfaces with PLIP using the PythonCall.jl package, allowing seamless integration of PLIP's robust algorithms.
Current Features
- Upload of two PDB files for comparison.
- Automated identification of potential ligands with user selection.
- Detection and quantification of hydrogen bonds for each complex.
- Generation of:
- A comparative summary table (CSV) highlighting common and differential H-bonds and interacting residues.
- A detailed list of all H-bonds for both complexes (CSV).
- A bar chart visually comparing H-bond counts per residue across the two complexes (PNG).
- An on-page analytical summary of key findings.
Future Development
juProt is an ongoing project. Future development plans include:
- Expanding comparative analysis to other interaction types (hydrophobic, pi-stacking, salt bridges, etc.).
- Enhanced visualization options, potentially including 2D comparative interaction diagrams.
- Allowing analysis of more than two complexes.
- User-configurable parameters for interaction detection.
Development Team
juProt was conceived and developed by:
Deepak S P, MSc Biotechnology
Siva V, MSc Biotechnology
Surya Sekaran, [PhD]
We also acknowledge the developers of the core libraries used in juProt, including Julia, Genie.jl, PythonCall.jl, PLIP, OpenBabel, and Plots.jl.
Open Source & Citation
juProt is an open-source project. The source code is available on GitHub at https://github.com/drbenedictpaul/juprot.
We encourage contributions and feedback from the community.
If you use juProt in your research, please cite:
[Manuscript is in communication. For now, please cite our GitHub repository.]
Contact/Feedback
For questions, suggestions, or to report issues, please visit our GitHub issues page at GitHub Issues or contact benedictpaulc@sriramachandra.edu.in.