WEBnma3

WEBnma3 performs normal mode analysis (NMA) on protein structures using elastic network models to characterize protein flexibility and identify low-frequency collective motions relevant to function.

Key Features:

• Elastic network model NMA: Computes normal modes from protein coordinate files using elastic network models to probe slow collective motions.
• Comparative NMA: Performs comparative NMA on sets of pre-aligned protein structures to assess flexibility conservation across related proteins.
• Input formats: Accepts sequence alignments in FASTA format together with corresponding coordinate files in PDB format.
• Pairwise dynamic comparison: Quantifies pairwise dynamic similarity using the Root Mean Squared Inner Product (RMSIP) and the Bhattacharyya Coefficient.
• Fluctuation and deformation analyses: Computes normalized squared atomic fluctuations and atomic deformation energies for per-residue and per-atom assessment.
• Correlation and overlap analyses: Provides inter-residue correlation calculations and overlap analysis to evaluate conformational change relationships.
• Vector field and mode visualization: Produces vector field representations and animations of the first six vibrational modes.
• Programmatic access: Exposes functionality via a SOAP-based web service for integration into computational workflows.
• Application architecture: Implements a modular architecture capable of handling large biomolecular assemblies such as transmembrane channels and virus capsids.

Scientific Applications:

• Comparative flexibility analysis: Assess conservation of dynamic behavior across protein families and superfamilies.
• Identification of functional motions: Detect soft, low-frequency normal modes that correspond to large-amplitude, functionally relevant movements.
• Dynamics of large assemblies: Analyze flexibility and collective motions in multi-domain proteins, transmembrane channels, and virus capsids.

Methodology:

Normal modes are calculated from user-provided PDB structure files using elastic network models; analyses explicitly include normalized squared atomic displacements, atomic deformation energies, inter-residue correlations, overlap analysis, vector field representations and animations of the first six vibrational modes, and pairwise comparisons using RMSIP and the Bhattacharyya Coefficient, with inputs accepted as FASTA alignments plus corresponding PDB files and programmatic access via SOAP.