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Protein flexibility prediction by an all‐atom mean‐field statistical theory
Author(s) -
Pandey B.P.,
Zhang Chi,
Yuan Xianzhang,
Zi Jian,
Zhou Yaoqi
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.041311005
Subject(s) - flexibility (engineering) , atom (system on chip) , mean field theory , field (mathematics) , statistical physics , physics , statistics , computer science , mathematics , quantum mechanics , embedded system , pure mathematics
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.