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Related Experiment Videos

Scoring docking models with evolutionary information.

Michael Tress1, David de Juan, Osvaldo Graña

  • 1Protein Design Group, CNB-CSIC, Cantoblanco, Madrid, Spain. mtress@cnb.uam.es <mtress@cnb.uam.es>

Proteins
|June 28, 2005
PubMed
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We developed methods using evolutionary information from multiple sequence alignments to predict protein interactions. This approach successfully generated acceptable models for 4 out of 12 targets in the CAPRI experiment.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Evolutionary biology

Background:

  • Protein interactions are crucial for cellular functions.
  • Predicting these interactions is vital for understanding biological systems.
  • Evolutionary information can enhance prediction accuracy.

Purpose of the Study:

  • To develop and apply methods for extracting evolutionary information from multiple sequence alignments.
  • To utilize this information for protein interaction network studies and prediction.
  • To evaluate the performance of these methods in the CAPRI (Critical Assessment of PRedicted Interactions) experiment.

Main Methods:

  • Extraction of evolutionary information from multiple sequence alignments.
  • Generation of protein docking models using Hex and GRAMM.

Related Experiment Videos

  • Selection of predictions based on evolutionary information and experimental evidence.
  • Application of methods to targets in Rounds 3, 4, and 5 of the CAPRI experiment.

    • Main Results:

    • Predictions were submitted for 7 out of 12 CAPRI targets.
    • Acceptable level models were successfully predicted for 4 targets.
    • The binding surface residues were identified for a fifth target.
    • The study highlights successes and limitations in predicting protein interactions.

    Conclusions:

    • Methods based on evolutionary information from multiple sequence alignments are effective for protein interaction prediction.
    • This approach aids in understanding protein interaction network evolution.
    • Further refinement is needed to address limitations in specific docking cases.