Protein flexibility prediction by an all-atom mean-field statistical theory

B. P. Pandey, Chi Zhang, Xianzhang Yuan, Jian Zi, Yaoqi Zhou

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

We extended a mean-field model to proteins with all atomic detail. The all-atom mean-field model was used to calculate the dynamic and thermodynamic properties of a three-helix bundle fragment of Staphylococcal protein A (Protein Data Bank [PDB] ID 1BDD) and α-spectrin SH3 domain protein (PDB ID 1SHG). We show that a model with all-atomic detail provides a significantly more accurate prediction of flexibility of residues in proteins than does a coarse-grained residue-level model. The accuracy of flexibility prediction is further confirmed by application of the method to 18 additional proteins with the largest size of 224 residues.

Original languageEnglish (US)
Pages (from-to)1772-1777
Number of pages6
JournalProtein Science
Volume14
Issue number7
DOIs
StatePublished - Jul 2005

Keywords

  • All-atom model
  • Mean-field statistical theory
  • Protein flexibility
  • Protein thermodynamics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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