WEBnma

WEBnma performs normal mode analysis (NMA) of protein structures using elastic network models to characterize protein flexibility and dynamics.

Key Features:

• Automated Comparative NMA: Performs comparative NMA on multiple pre-aligned protein structures using sequence alignments in FASTA format and coordinate files in PDB format.
• Dynamic Comparison Metrics: Provides pairwise comparison of protein dynamics using the Root Mean Squared Inner Product and the Bhattacharyya Coefficient.
• Mode Representations and Analyses: Computes inter-residue correlations, overlap analyses of conformational changes, and representations of protein motion including vector field representations and animations of the first six vibrational modes.

Scientific Applications:

• Low-frequency (soft) mode analysis: Investigates low-frequency normal modes to identify the largest and most functionally relevant movements within proteins.
• Large macromolecular assemblies: Studies collective motions in systems such as transmembrane channels and virus capsids to relate dynamics to function.

Methodology:

Normal mode analysis using elastic network models, calculation of normalized squared atomic displacements, inter-residue correlation and overlap analyses, and pairwise comparisons using Root Mean Squared Inner Product and Bhattacharyya Coefficient applied to user-provided PDB structures and FASTA alignments.