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Related Experiment Video

Updated: May 20, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer.

Maria U Johansson1, Vincent Zoete, Olivier Michielin

  • 1Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

BMC Bioinformatics
|July 25, 2012
PubMed
Summary

This study introduces a new tool for identifying structural motifs in proteins, making it easier to find common patterns across diverse protein structures. This advancement aids in understanding protein fold stabilization and evolution.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein sequence and fold recognition are well-established fields with ample software tools.
  • Structural motif recognition is less developed and underutilized due to a lack of accessible software.

Purpose of the Study:

  • To develop and present an extension of DeepView/Swiss-PdbViewer for defining and searching structural motifs.
  • To demonstrate the utility of this tool in identifying conserved structural patterns within protein databases.

Main Methods:

  • Extension of the DeepView/Swiss-PdbViewer software.
  • Development of methods for defining and searching custom structural motifs.
  • Application to large protein structure databases.

Main Results:

  • Common structural motifs involved in stabilizing protein folds were identified.
  • These motifs were found in evolutionarily and structurally unrelated proteins.
  • Motifs were also detected in deeply buried protein regions, irrespective of obvious functional links.

Conclusions:

  • The developed tool enables the identification of recurrent residue arrangements with potential structural implications.
  • Custom motif definition and searching are now accessible to both experts and non-experts without complex installations.
  • This facilitates broader research into protein structure and evolution.