Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

J Vis Exp. 2017 Jul 16;(125):55640. doi: 10.3791/55640.


We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis. This integrated functionality provides a complete online workflow for investigating sequence-structure-dynamic relationships within protein families and superfamilies.

Publication types

  • Video-Audio Media

MeSH terms

  • Amino Acid Sequence / genetics*
  • Data Interpretation, Statistical
  • Programming Languages*
  • Proteins / chemistry*
  • Sequence Alignment / methods*


  • Proteins