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Caspases01:24

Caspases

Caspase, a family of cysteine proteases, serve as effectors in apoptosis. The ced3 gene in C.elegans was first identified to be involved in apoptosis. This gene encodes the ced-3 caspase that is similar to the interleukin-1-beta converting enzyme or ICE in mammals. In addition to apoptosis, caspases also function in the inflammatory response. Inflammatory caspases are essential in activating pro-inflammatory cytokines that recruit immune cells and block the replication of pathogens inside cells.
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Conservation of Protein Domains Over Different Proteins

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Measuring Caspase Activity Using a Fluorometric Assay or Flow Cytometry
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Target domain definition and classification in CASP8.

Michael L Tress1, Iakes Ezkurdia, Jane S Richardson

  • 1Structural and Computational Biology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. mtress@cnio.es

Proteins
|July 16, 2009
PubMed
Summary
This summary is machine-generated.

The Critical Assessment of protein Structure Prediction (CASP) experiments rely on experimentally determined protein structures. CASP8 results indicate that protein structure prediction targets are becoming easier to predict, with most classified as template-based modeling.

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Area of Science:

  • * Computational biology
  • * Structural biology
  • * Bioinformatics

Background:

  • * CASP experiments necessitate experimentally determined protein structures for assessment.
  • * Structural genomics initiatives supply the majority of these structures.
  • * Target structures must be segmented into domains and categorized for prediction assessment.

Purpose of the Study:

  • * To analyze the classification and prediction trends in the CASP8 experiment.
  • * To categorize target domains into template-based and free modeling assessments.
  • * To evaluate the ease of protein structure prediction over time.

Main Methods:

  • * Protein structures were divided into domains for assessment.
  • * Domains were classified into "template-based modeling" or "free modeling" categories.
  • * Classification relied on structural similarity to known templates in the Protein Data Bank (PDB) and model-building methods.

Main Results:

  • * The Critical Assessment of protein Structure Prediction (CASP) experiment in CASP8 involved 164 assessment units.
  • * The vast majority (164 units) were classified as template-based modeling.
  • * Only 10 target domains were classified as free modeling, with 3 assessed in both categories.

Conclusions:

  • * CASP8 targets confirmed a trend of increasing ease in protein structure prediction since CASP5.
  • * The majority of CASP8 targets were amenable to template-based modeling approaches.
  • * Protein structure prediction is becoming more accurate and accessible.