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Protein structure refinement by optimization.

Martin Carlsen1, Peter Røgen1

  • 1Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, DK-2800, Denmark.

Proteins
|June 23, 2015
PubMed
Summary

This study introduces an iterative strategy to enhance protein structure prediction by improving decoy convergence. Optimized decoys are added to training data, leading to significantly better results in protein modeling.

Keywords:
funnel sculptingiterative methodsknowledge-based potentialsoptimizationprotein structure refinement

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Knowledge-based protein potentials are crucial for improving protein model quality, essential for biological and pharmaceutical research.
  • Current potentials efficiently rank protein decoys but do not guarantee convergence to native structures via energy minimization.

Purpose of the Study:

  • To introduce an iterative strategy for enhancing the convergence of protein decoy structures.
  • To improve the accuracy of knowledge-based protein potentials through an iterative refinement process.

Main Methods:

  • Developed an iterative strategy that incorporates energy-optimized decoys into the training pool for subsequent potential construction.
  • Formulated a potential in Cartesian coordinates with fixed backbone and hydrogen-bonding potentials.
  • Employed a variable coarse-grained carbon alpha potential with a novel b-spline based solvent potential.
  • Utilized explicit gradient and Hessian for efficient energy optimization.

Main Results:

  • Demonstrated significantly improved decoy convergence on high-resolution decoys (Titan) and refinement targets (CASP).
  • The iterative approach effectively refines protein structure prediction models.

Conclusions:

  • The proposed iterative strategy offers a substantial improvement in protein decoy convergence.
  • This method enhances the utility of knowledge-based potentials for accurate protein structure modeling.