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. 2002 Nov;11(11):2714-26.
doi: 10.1110/ps.0217002.

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

Hongyi Zhou  1 , Yaoqi Zhou
Affiliations

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

Hongyi Zhou et al. Protein Sci. 2002 Nov.

Erratum in

  • Protein Sci. 2003 Sep;12(9):2121

Abstract

The distance-dependent structure-derived potentials developed so far all employed a reference state that can be characterized as a residue (atom)-averaged state. Here, we establish a new reference state called the distance-scaled, finite ideal-gas reference (DFIRE) state. The reference state is used to construct a residue-specific all-atom potential of mean force from a database of 1011 nonhomologous (less than 30% homology) protein structures with resolution less than 2 A. The new all-atom potential recognizes more native proteins from 32 multiple decoy sets, and raises an average Z-score by 1.4 units more than two previously developed, residue-specific, all-atom knowledge-based potentials. When only backbone and C(beta) atoms are used in scoring, the performance of the DFIRE-based potential, although is worse than that of the all-atom version, is comparable to those of the previously developed potentials on the all-atom level. In addition, the DFIRE-based all-atom potential provides the most accurate prediction of the stabilities of 895 mutants among three knowledge-based all-atom potentials. Comparison with several physical-based potentials is made.

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Figures

Fig. 1.
Fig. 1.
Scaling behavior of uniformly distributed heavy atoms in 1011 spheres. Number of pairs was counted in every 1 Å shell, and r is the middle point of the shell. (a) Relative fluctuation δ, and (b) reduced distance-dependent function f(r) = N(r)/rα.
Fig. 2.
Fig. 2.
The experimentally measured changes in stability versus theoretically predicted ones in a database of 895 large-to-small mutations. (a) RAPDF, (b) atomic KBP, (c) DFIRE-A. Lines represent the results from linear regression fit. The correlation coefficients are 0.52, 0.55, and 0.67 for RAPDF, atomic KBP and DFIRE-A, respectively.
Fig. 3.
Fig. 3.
The distance dependence of three knowledge-based potentials (a) between atom N of residue Cys and atom O of residue Trp, and (b) between atom Cα of residue Ile and atom Cδ2 of residue Leu.
Fig. 4.
Fig. 4.
The distance dependence of three knowledge-based potentials (a) between Cβ atoms of Leu and Ile residues, and (b) between Cβ atoms of Leu and Asp residues.
Fig. 5.
Fig. 5.
The distance dependence of NexpRAPDF/KBP(r)/NexpDFIRE-A(r).
See this image and copyright information in PMC

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