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ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.

Patrice Gouet1, Xavier Robert, Emmanuel Courcelle

  • 1Laboratoire de BioCristallographie, IBCP-CNRS UMR 5086 UCBL, 7 passage du Vercors, 69367 Lyon Cedex 07, France. p.gouet@ibcp.fr

Nucleic Acids Research
|June 26, 2003
PubMed
Summary
This summary is machine-generated.

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ESPript and ENDscript are powerful tools for visualizing protein sequence alignments with secondary structures. They integrate with other bioinformatics resources, aiding in the analysis of protein sequence and structure conservation.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • ESPript, developed in 1993, visualizes multiple sequence alignments with secondary structures.
  • Web servers for ESPript (1999) and ENDscript (2002) were created to enhance accessibility and functionality.
  • These tools integrate with major bioinformatics web tools like ProDom, PredictProtein, and NPS@.

Purpose of the Study:

  • To present ESPript and ENDscript, bioinformatics tools for generating informative figures of protein sequence alignments.
  • To highlight the capabilities of ENDscript in integrating sequence and 3D structural information.
  • To provide a comprehensive visualization of sequence and structure conservation.

Main Methods:

  • ESPript utilizes PostScript for displaying alignments with secondary structures.

Related Experiment Videos

  • ENDscript integrates sequence analysis tools (BLAST, Clustal) and structure analysis tools (DSSP, CNS, MOLSCRIPT).
  • Structure superposition is performed using PROFIT, and figures are generated with BOBSCRIPT, showing conservation along the Calpha trace.

    • Main Results:

    • Generation of figures displaying multiple sequence alignments with secondary structure elements.
    • Integration of 3D structural information with sequence alignments from a single Protein Data Bank identifier.
    • Visualization of sequence and structure conservation across related protein structures.

    Conclusions:

    • ESPript and ENDscript offer robust solutions for visualizing and analyzing protein sequence and structure relationships.
    • The tools facilitate the understanding of conserved regions in proteins by combining sequence and structural data.
    • These resources are valuable for researchers in bioinformatics and structural biology, available at http://genopole.toulouse.inra.fr/ESPript.