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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...

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TarO: a target optimisation system for structural biology.

Ian M Overton1, C A Johannes van Niekerk, Lester G Carter

  • 1School of Life Sciences Research, University of Dundee, Dow Street, Dundee, UK.

Nucleic Acids Research
|April 4, 2008
PubMed
Summary
This summary is machine-generated.

TarO is a bioinformatics tool that analyzes protein sequences using 17 algorithms and 8 databases. It predicts properties like crystallization propensity and disorder, aiding structural biology research.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Selecting appropriate proteins and domains is crucial for structural biology.
  • Bioinformatic analyses are essential for characterizing protein properties and identifying suitable targets.
  • Existing tools may lack integrated analysis pipelines for target selection.

Purpose of the Study:

  • To provide a centralized bioinformatics resource for selecting protein targets for structural biology.
  • To integrate multiple analysis algorithms and databases for comprehensive protein characterization.
  • To streamline the process of identifying and annotating potential structural biology targets.

Main Methods:

  • Utilizes 17 distinct bioinformatics algorithms for sequence analysis.
  • Compares sequences against 8 curated biological databases.
  • Employs a high-performance computing cluster for analysis execution.
  • Integrates results into a searchable database with a web-based interface.

Main Results:

  • Identifies putative protein homologues, including orthologues.
  • Predicts key protein properties such as crystallization propensity and disorder.
  • Generates annotated multiple sequence alignments (MSAs) for interactive editing in Jalview.
  • Facilitates access to external annotation resources like UniProt and COG.

Conclusions:

  • TarO serves as a valuable single point of reference for structural biology target selection.
  • The integrated approach simplifies the identification and characterization of proteins for experimental study.
  • Future developments aim to expand analysis capabilities and integrate with protein information management systems.