WEBnma

WEBnma is a web-based tool for predicting and analyzing flexibility in protein structures using Normal Mode Analysis (NMA). It is part of the ELIXIR Norway infrastructure services and is aimed at structural biology researchers who need to study large-scale conformational motions in biomolecules without the computational cost of full molecular dynamics simulations.

WEBnma is also a consortium member of the Protein Data Bank in Europe — Knowledge Base (PDBe-KB), meaning its results are integrated into PDBe-KB aggregated views for PDB entries. Normal Mode Analysis computes low-frequency vibrational modes to identify functionally relevant motions, making it applicable to understanding protein function, dynamics, and interactions.

Key Features

• Normal Mode Analysis — computes low-frequency vibrational modes to identify functionally relevant motions in protein structures
• Flexibility prediction — identifies flexible and rigid regions within a protein chain
• Comparative analysis — supports side-by-side comparison of the dynamics of multiple protein structures
• Visualization — provides interactive visualization of normal modes and predicted motions
• PDB integration — allows structures to be loaded directly from the Protein Data Bank by ID
• PDBe-KB consortium membership — analysis results are incorporated into PDBe-KB aggregated views for PDB entries

Workflow

1. Access the WEBnma analysis tool via its web interface
2. Upload a PDB file or enter a PDB identifier to load a protein structure
3. Run the Normal Mode Analysis and explore the computed flexibility profiles
4. Use the comparative mode to analyze dynamics across related structures

WEBnma is accessible as a web service and operates within the ELIXIR Norway infrastructure. Its integration with PDBe-KB means that flexibility predictions for PDB entries are available through the broader PDBe-KB knowledge base.