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April 25, 2005Proteins Structure Function and Bioinformatics

A consistent set of statistical potentials for quantifying local side‐chain and backbone interactions

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QFQiaojun FangDSDavid Shortle

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Overview

Computational structural analysis demonstrates accurate identification of native protein conformations using local statistical potentials, highlighting their utility in structural refinement.

Key Points

  • To develop and evaluate an extended set of statistical potentials that quantify local interactions between amino acid side-chains and both the polypeptide backbone and adjacent side-chains.
  • Augmented phi/psi/chi1 backbone-flanking propensities with three terms: distance-dependent side-chain-to-backbone interactions (i +/- 2 to 4), distance-dependent side-chain-to-side-chain interactions (i to i + 1 to 4), and orientation-dependent side-chain interactions.
  • Evaluated energy terms using matrix information content, a 15-mer fragment threading test across 232,000 alternative conformations, and discrimination tests on 20 sets of all-atom Rosetta decoys (1,700–1,900 conformations each).
  • Pseudo free energy terms ranged from -0.4 to -0.5 kcal/mol per residue for phi/psi/chi1 propensities and from -0.15 to -0.6 kcal/mol per residue for each of the three additional distance- and orientation-dependent terms.
  • The combined four-term energy function correctly identified native 15-mer fragments over 40% of the time from 232,000 decoys and ranked the native structure lowest in 14 of 20 Rosetta decoy sets.
  • The scoring function reliably distinguished high-resolution X-ray crystal structures from NMR solution structures based on fine details of local geometry.

Cite This Study

Fang et al. (2005) studied this question.

synapsesocial.com/papers/6a7571d01646b2abe5037377https://doi.org/10.1002/prot.20482
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