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Related Experiment Videos

3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs.

Steven P Bennett1, Lin Lu, Douglas L Brutlag

  • 1Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA.

Nucleic Acids Research
|June 26, 2003
PubMed
Summary

We developed 3MATRIX and 3MOTIF, web tools that visualize protein sequence motifs in 3D. These tools help understand protein function and structure by highlighting conserved amino acids within their structural context.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Computational methods like sequence alignment aid in protein family grouping and functional annotation.
  • Identifying conserved amino acids is crucial, but their specific roles require further investigation.

Purpose of the Study:

  • To present 3MATRIX and 3MOTIF, web-based systems for visualizing sequence motifs in a 3D structural context.
  • To provide a flexible platform for exploring protein sequence and motif information.

Main Methods:

  • Users can input sequences, keywords, structures, or motifs (PROSITE patterns, eMOTIFs, regular expressions) into 3MOTIF.
  • 3MATRIX accepts eMATRIX position-specific scoring matrices or converts multiple sequence alignment blocks into eMATRIX for visualization.

Related Experiment Videos

  • Query motifs are used to search a protein structure database, highlighting matches in 3D and displaying properties like conservation and solvent accessibility.

    • Main Results:

    • The 3MATRIX and 3MOTIF systems enable visualization of sequence motifs within their native 3D protein structures.
    • Visualizations incorporate sequence conservation and solvent accessible surface area using color-coding.
    • The system facilitates the exploration of motif properties in relation to protein structure.

    Conclusions:

    • 3MATRIX and 3MOTIF offer a novel approach to understanding protein sequence motifs by integrating them into 3D structural visualizations.
    • These tools enhance the annotation of new proteins and the study of protein families.
    • The visualization of conserved residues and their structural context aids in deciphering functional and structural roles.