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WEBnm@ v2.0: Web server and services for comparing protein flexibility.

Sandhya P Tiwari1,2, Edvin Fuglebakk3, Siv M Hollup4

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Summary

WEBnm@ v2.0 offers comparative normal mode analysis (NMA) for multiple protein structures. This tool helps assess protein flexibility and dynamics within families, aiding in understanding structure-function relationships.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein dynamics

Background:

  • Normal mode analysis (NMA) using elastic network models is a cost-effective method for characterizing protein flexibility and dynamics.
  • Comparing protein motions across homologs and functional groups provides insights into the dynamics-function relationship.
  • Analyzing normal modes from evolutionary related proteins facilitates comparative studies.

Purpose of the Study:

  • To develop an automated tool for comparative normal mode analysis (NMA) of multiple protein structures.
  • To provide a web server for easy comparison of protein dynamics and flexibility within sets of proteins.

Main Methods:

  • Developed an automated web server (WEBnm@) for comparative NMA.
  • Users submit sequence alignments (FASTA) and PDB coordinate files.
  • Calculates normalized squared atomic fluctuations and atomic deformation energies.
  • Employs Root Mean Squared Inner Product and Bhattacharyya Coefficient for pairwise dynamics comparison.

Main Results:

  • WEBnm@ v2.0 enables automated comparative NMA for pre-aligned protein structures.
  • Provides graphical comparisons of atomic fluctuations and deformation energies.
  • Offers pairwise comparison of protein dynamics using RMSIP and Bhattacharyya Coefficient.
  • Includes upgraded NMA functionality for single structures with new visualizations and analysis methods.

Conclusions:

  • WEBnm@ v2.0 is a unique online tool for comparative NMA of multiple protein structures.
  • Facilitates assessment of protein flexibility within families and superfamilies.
  • Aids in understanding how protein structures move and conserve flexibility across related proteins.