Welcome to ProtLego! An Open-source Python Library for Chimera Design and Analysis

ProtLego is a tool that enables constructing protein chimeras and its structural analysis. ProtLego is writen in Python, so it facilitates that other scientists can extend it to their needs.

With ProtLego, it is possible to go from a pair of PDBs that share a structural fragment in common, to build all possible chimeras between the two, rank them with the AMBER or CHARMM molecular mechanics forcefields, and analyze their structural features (hydrogen networks, salt bridges, hydrophobic clusters…etc.)

Code

• Building Chimeras
• Chimera Class
• Fetching hits from Fuzzle
• Networks
• Energy scoring
• Clusters
• HH-networks
• Salt-bridges
• Further structural analysis

User Guide

• Installation
• PIP installation
• CONDA installation
• Setup
• Installing from environment file
• Troubleshooting
• Visit Fuzzle

Tutorials

• Introduction to Jupyter-notebooks and Python primer
  • How to use Jupyter-notebook
  • Programming basics with Python
• Fetching from the Fuzzle database
  • 1. Fetching from ID
  • 2. Search all the hits that contain a specific domain
  • 3. Fetch by parents (finding a hit between two domains)
  • 4. Fetching two groups
  • 5. Fetching subspaces
• Drawing networks
  • 1. Drawing relationships between two superfamilies
• Building chimeras
  • Chimera-Building using Protlego
• Energy scoring
• Structural analysis of chimeras
  • 1. Hydrophobic cluster analysis
  • 2. Salt bridges analysis
  • 3. Hydrogen Network analysis
  • 4. Further structural analysis

Publications

Protlego: A Python package for the analysis and design of chimeric proteins. Noelia Ferruz, Jakob Noske, Birte Höcker.