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Template-based modeling and ab-initio docking using CoDock in CAPRI.

Ren Kong1, Ran-Ran Liu1, Xi-Ming Xu1,2

  • 1Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China.

Proteins
|March 18, 2020
PubMed
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A new hybrid docking strategy, CoDock, integrates template-based modeling and ab-initio docking. This approach demonstrated strong performance in predicting molecular interactions for protein-oligosaccharide targets in recent computational challenges.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Accurate molecular docking is essential for understanding biological processes and drug discovery.
  • Developing robust docking programs requires integrating template-based modeling, global sampling, and precise scoring.

Purpose of the Study:

  • To introduce and evaluate a hybrid docking strategy, CoDock, combining template-based and ab-initio methods.
  • To assess the performance of CoDock in the seventh edition of the Critical Assessment of Prediction of Interactions (CAPRI) and the CASP13-CAPRI experiment.

Main Methods:

  • CoDock employs a hybrid docking strategy integrating template-based modeling with an ab-initio docking protocol.
  • The strategy was applied to docking and scoring experiments for various targets in CAPRI rounds 38-45 and CASP13-CAPRI (round 46).
Keywords:
CAPRICASP-CAPRICoDockcomplex structure predictionmolecular docking

Related Experiment Videos

Main Results:

  • CoDock achieved acceptable or better models in top submissions for 8/16 targets as predictors and 9/16 as scorers in CAPRI rounds 38-45.
  • Notably, all protein-oligosaccharide targets yielded acceptable models.
  • In CASP13-CAPRI, acceptable or better models were obtained for 10/20 targets as predictors and 11/20 as scorers within the top 5 submissions.

Conclusions:

  • The hybrid docking strategy, CoDock, shows significant efficiency and adaptability in addressing diverse molecular interaction challenges.
  • Performance was particularly strong for protein-oligosaccharide interactions, while protein-peptide systems and highly complex targets presented greater difficulties.