Probabilistic search and energy guidance for biased decoy sampling in ab initio protein structure prediction

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1162-75. doi: 10.1109/TCBB.2013.29.

Abstract

Adequate sampling of the conformational space is a central challenge in ab initio protein structure prediction. In the absence of a template structure, a conformational search procedure guided by an energy function explores the conformational space, gathering an ensemble of low-energy decoy conformations. If the sampling is inadequate, the native structure may be missed altogether. Even if reproduced, a subsequent stage that selects a subset of decoys for further structural detail and energetic refinement may discard near-native decoys if they are high energy or insufficiently represented in the ensemble. Sampling should produce a decoy ensemble that facilitates the subsequent selection of near-native decoys. In this paper, we investigate a robotics-inspired framework that allows directly measuring the role of energy in guiding sampling. Testing demonstrates that a soft energy bias steers sampling toward a diverse decoy ensemble less prone to exploiting energetic artifacts and thus more likely to facilitate retainment of near-native conformations by selection techniques. We employ two different energy functions, the associative memory Hamiltonian with water and Rosetta. Results show that enhanced sampling provides a rigorous testing of energy functions and exposes different deficiencies in them, thus promising to guide development of more accurate representations and energy functions.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computer Simulation
  • Energy Transfer*
  • Models, Chemical*
  • Models, Molecular*
  • Models, Statistical*
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / ultrastructure*
  • Sample Size

Substances

  • Proteins