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DINAMO: interactive protein alignment and model building.

J Bentz1, A Baucom, M Hansen

  • 1Departments of Biology, Computer Science and Chemistry & Biochemistry, University of California, Santa Cruz, CA 95064, USA.

Bioinformatics (Oxford, England)
|May 13, 1999
PubMed
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DINAMO is a novel tool that aids protein structure prediction by interactively aligning sequences and evaluating models. It uses visual cues for rapid assessment, facilitating comparative modeling and fold recognition.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Protein structure prediction is crucial for understanding protein function.
  • Comparative modeling and fold recognition are key methods in structure prediction.
  • Interactive tools are needed to optimize alignment and model evaluation.

Purpose of the Study:

  • To introduce DINAMO, an interactive tool for protein alignment and model evaluation.
  • To facilitate the process of protein structure prediction.
  • To couple multiple sequence alignment editing with molecular graphics display.

Main Methods:

  • DINAMO dynamically couples a multiple sequence alignment editor with a molecular graphics display.
  • It employs analysis tools providing visual cues (color, shape) for rapid evaluation.

Related Experiment Videos

  • Analysis includes residue conservation, properties, environmental preference, and secondary structure propensity.

    • Main Results:

    • DINAMO was used to build a protein model for the CASP3 contest.
    • The tool allows users to optimize alignments and models based on protein structure heuristics.
    • Visual feedback enables efficient assessment of alignment and model quality.

    Conclusions:

    • DINAMO enhances the efficiency and accuracy of protein structure prediction.
    • The interactive approach simplifies complex alignment and modeling tasks.
    • The tool is freely available, promoting wider adoption in the research community.