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ICM-DISCO docking by global energy optimization with fully flexible side-chains.

Juan Fernández-Recio1, Maxim Totrov, Ruben Abagyan

  • 1Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Proteins
|June 5, 2003
PubMed
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The ICM-DISCO protein-protein docking method automates complex molecular interactions. It successfully predicts binding poses for many targets, especially when interfaces remain unchanged during docking.

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein-protein interactions are crucial for biological processes.
  • Accurate prediction of protein complex structures is essential for understanding function and disease.
  • Existing computational methods face challenges in handling conformational changes upon binding.

Purpose of the Study:

  • To present and evaluate the ICM-DISCO (Docking and Interface Side-Chain Optimization) method for automated protein-protein docking.
  • To assess the method's performance in predicting protein complex structures, including cases with induced fit.

Main Methods:

  • ICM-DISCO employs a two-step stochastic global energy optimization approach.
  • Step 1: Rigid docking of an all-atom ligand to soft receptor potentials.

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  • Step 2: Global optimization of interface side-chains for top solutions, incorporating experimental data for filtering.

    • Main Results:

    • The method achieved near-perfect accuracy for complexes with rigid interfaces.
    • For targets with induced fit, ICM-DISCO identified good solutions (>50% correct contacts) within the top five predictions for 3 out of 7 cases.
    • The algorithm effectively handles side-chain rearrangements but shows limitations with significant backbone changes.

    Conclusions:

    • ICM-DISCO is a fully automated and global protein-protein docking method.
    • The approach is effective for predicting structures with minimal interface rearrangement.
    • Further development is needed to improve accuracy for complexes involving large backbone changes.