GANDivAWeb: a web server for detecting early folding units ("foldons") from protein 3D structures

Area of Science:

• Structural biology
• Computational biology
• Protein science

Background:

• Proteins fold via autonomous folding units (AFUs), also known as foldons.
• Understanding AFUs is crucial for protein engineering and comprehending protein folding.
• AFUs serve as model systems for studying protein structural organization.

Purpose of the Study:

• To develop a webserver, GANDivAWeb, for identifying foldons in protein networks.
• To provide a user-friendly tool for analyzing protein modularity and early folding units.

Main Methods:

• Utilized a global network partitioning algorithm to identify protein modules.
• Developed the GANDivAWeb server with functionalities for database exploration and PDB file analysis.
• Integrated visualization tools for module decomposition, connectivity, hydrophobicity, and RASA.

Main Results:

• The GANDivAWeb server successfully identifies modules correlating with AFUs.
• The server offers three distinct functionalities for protein analysis.
• Results include detailed visualizations of protein structure and folding properties.

Conclusions:

• GANDivAWeb is a valuable tool for protein folding research and protein engineering.
• The server identifies AFUs and critical residues involved in protein folding.
• Future work includes studying topological determinants of protein folding using the tool.