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

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

doi:10.1110/ps.041311005

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 journal › Article › peer-review

18 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 language	English (US)
Pages (from-to)	1772-1777
Number of pages	6
Journal	Protein Science
Volume	14
Issue number	7
DOIs	https://doi.org/10.1110/ps.041311005
State	Published - Jul 2005
Externally published	Yes

Keywords

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

ASJC Scopus subject areas

Biochemistry
Molecular Biology

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10.1110/ps.041311005

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title = "Protein flexibility prediction by an all-atom mean-field statistical theory",

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.",

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year = "2005",

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language = "English (US)",

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T1 - Protein flexibility prediction by an all-atom mean-field statistical theory

AU - Pandey, B. P.

AU - Zhang, Chi

AU - Yuan, Xianzhang

AU - Zi, Jian

AU - Zhou, Yaoqi

PY - 2005/7

Y1 - 2005/7

N2 - 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.

AB - 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.

KW - All-atom model

KW - Mean-field statistical theory

KW - Protein flexibility

KW - Protein thermodynamics

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JO - Protein Science

JF - Protein Science

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

Abstract

Keywords

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