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Related Experiment Videos

Consensus alignment server for reliable comparative modeling with distant templates.

Jahnavi C Prasad1, Sandor Vajda, Carlos J Camacho

  • 1Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA.

Nucleic Acids Research
|June 25, 2004
PubMed
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The Consensus server generates reliable protein sequence alignments for comparative modeling, even with low sequence identity. It predicts accurate regions for modeling, improving structural reliability for critical applications.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Comparative modeling is crucial for predicting protein structures.
  • Accurate sequence alignments are fundamental for reliable comparative modeling.
  • Identifying reliable alignment regions is challenging, especially at low sequence identities.

Purpose of the Study:

  • To develop a server (Consensus) for high-quality protein sequence alignments.
  • To identify reliable alignment regions for comparative modeling.
  • To improve the accuracy of protein structure prediction through enhanced alignments.

Main Methods:

  • The server integrates outputs from five distinct alignment algorithms.
  • It generates a consensus alignment with position-specific reliability scores.

Related Experiment Videos

  • Predictions highlight regions suitable for accurate modeling.

    • Main Results:

    • The Consensus server produces alignments effective even at 5% target-template sequence identity.
    • Models built using server predictions achieve within 3 Å RMSD of crystal structures.
    • Validation on homologous protein pairs confirms the method's robustness.

    Conclusions:

    • The Consensus server enhances the reliability of comparative modeling.
    • It provides valuable predictions for modelers prioritizing structural accuracy.
    • The tool is accessible online for broader use in structural biology research.