Introduction
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 a consortium member of the Protein Data Bank in Europe — Knowledge Base (PDBe-KB).
Normal Mode Analysis provides a computationally efficient way to study large-scale conformational motions in biomolecules, making it valuable for understanding protein function, dynamics, and interactions without requiring expensive molecular dynamics simulations.
Key Features
- Normal Mode Analysis — compute low-frequency vibrational modes to identify functionally relevant motions in protein structures
- Flexibility prediction — identify flexible and rigid regions within a protein chain
- Comparative analysis — compare the dynamics of multiple protein structures side by side
- Visualization — interactive visualization of normal modes and predicted motions
- PDB integration — load structures directly from the Protein Data Bank by ID
- PDBe-KB consortium member — results are integrated into the PDBe-KB aggregated views for PDB entries
Getting Started
- Visit WEBnma to access the analysis tool
- Upload a PDB file or enter a PDB identifier to load a protein structure
- Run the Normal Mode Analysis and explore the computed flexibility profiles
- Use the comparative mode to analyze dynamics across related structures