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Related Experiment Videos

Docking and scoring protein complexes: CAPRI 3rd Edition.

Marc F Lensink1, Raúl Méndez, Shoshana J Wodak

  • 1Centre de Biologie Structurale et Bioinformatique, CP 263, BC6, Université Libre de Bruxelles, Blvd du Triomphe, 1050 Bruxelles, Belgium.

Proteins
|October 9, 2007
PubMed
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Predicting protein-protein interactions at the atomic scale is challenging, especially modeling protein flexibility. Current scoring functions need improvement for accurate protein complex prediction.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • The Critical Assessment of PRedicted Interactions (CAPRI) experiment assesses protein-protein interaction prediction methods.
  • Previous CAPRI rounds have highlighted challenges in modeling protein flexibility and scoring interaction models.

Purpose of the Study:

  • To evaluate the performance of protein-protein interaction prediction methods at the atomic scale using blind predictions from CAPRI Rounds 6-12.
  • To assess the effectiveness of scoring functions in identifying correct protein complex models.

Main Methods:

  • Analysis of 1994 blind docking predictions submitted by 63 groups and 8 servers for 9 protein complexes.
  • Evaluation of 305 models submitted by 15 groups for a scoring experiment using 5 targets.

Related Experiment Videos

  • Predictions were initiated from unbound structures or homology models, requiring modeling of conformational changes.

    • Main Results:

    • 31 groups achieved acceptable to medium accuracy for most targets, but only one achieved high accuracy.
    • No method successfully modeled the large conformational changes required for the homodimer target.
    • Scoring experiment participants could identify correct association modes but struggled to pinpoint the best models, indicating insufficient scoring sensitivity.

    Conclusions:

    • Modeling protein flexibility remains a significant challenge in protein-protein interaction prediction.
    • Current scoring functions require further development to accurately rank predicted protein complex models.
    • Ongoing efforts in CAPRI aim to improve scoring functions and flexibility modeling for better protein assembly predictions.