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Related Concept Videos

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Advances in template-based protein docking by utilizing interfaces towards completing structural interactome.

Serena Muratcioglu1, Emine Guven-Maiorov1, Özlem Keskin1

  • 1Department of Chemical and Biological Engineering, Koc University, 34450 Istanbul, Turkey; Center for Computational Biology and Bioinformatics, Koc University, 34450 Istanbul, Turkey.

Current Opinion in Structural Biology
|November 6, 2015
PubMed
Summary
This summary is machine-generated.

Template-based docking (TBD) methods leverage known protein complex structures to model protein-protein interactions (PPIs). Interface-based TBD methods are effective, but more template proteins are needed to improve structural coverage and accuracy.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • The growing number of determined protein complex structures enhances template-based docking (TBD) for modeling protein-protein interactions (PPIs).
  • TBD methods use existing protein complex structures as templates to predict the quaternary structure of target proteins.
  • Interface-based TBD methods are gaining traction due to the reusability of protein interface regions.

Purpose of the Study:

  • To describe the utilization of available template interfaces for generating structural models of protein interactions.
  • To discuss the performance of interface-based TBD methods at a large scale.
  • To highlight the importance of considering multiple conformations for enhancing prediction accuracy.

Main Methods:

  • Utilizing known protein complex structures as templates for predicting protein-protein interactions.
  • Employing interface-based approaches that leverage reusable interface regions.
  • Analyzing the performance of template-based docking methods on large datasets.

Main Results:

  • A majority of protein complexes can be modeled using existing Protein Data Bank (PDB) structures.
  • Some studies suggest a need for expanded template protein databases to increase structural coverage of PPIs.
  • The performance of interface TBD methods at large scale and the impact of multiple conformations on accuracy are discussed.

Conclusions:

  • Template-based docking, particularly interface-based methods, is a powerful approach for modeling protein-protein interactions.
  • Further development and expansion of template databases are crucial for improving the structural coverage of PPIs.
  • Incorporating multiple conformations is significant for enhancing the accuracy of protein interaction modeling.