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Related Experiment Videos

Tools for integrated sequence-structure analysis with UCSF Chimera.

Elaine C Meng1, Eric F Pettersen, Gregory S Couch

  • 1Computer Graphics Laboratory, University of California San Francisco, 600 16th Street, San Francisco, CA 94143-2440, USA. meng@cgl.ucsf.edu

BMC Bioinformatics
|July 14, 2006
PubMed
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UCSF Chimera software enhances protein structure-function research by integrating sequence and structure data. New tools enable novel structure superposition and alignment generation for comparative analysis.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Protein structure-function research relies on comparing related structures and their sequence alignments.
  • Existing tools often lack deep integration between sequence and structure data.
  • There is a need for interactive visualization tools that facilitate data crosstalk and interoperability.

Purpose of the Study:

  • To describe enhancements to UCSF Chimera for integrated sequence and structure analysis.
  • To provide tools for deep integration of sequence and structure data.
  • To enable data manipulation based on either sequence or structure information.

Main Methods:

  • Enhancements to UCSF Chimera, a molecular graphics program.
  • Automatic association of protein structures with imported sequence alignments.

Related Experiment Videos

  • Development of a novel structure superposition method using sequence and secondary structure.
  • Implementation of a tool for constructing structure-based sequence alignments.

    • Main Results:

    • UCSF Chimera offers integrated tools for interactive sequence and structure analysis.
    • A new method allows structure superposition even with low sequence identity.
    • Structure-based sequence alignments can be generated from protein superpositions.
    • Chimera is extensible and supports user-specific data integration.

    Conclusions:

    • The described tools are applicable to diverse protein structure and sequence comparison problems.
    • UCSF Chimera is user-friendly, well-documented, and accessible to a broad scientific audience.
    • The software is freely available for non-commercial use on multiple platforms.