期刊
PROTEIN SCIENCE
卷 11, 期 11, 页码 2714-2726出版社
WILEY
DOI: 10.1110/ps.0217002
关键词
knowledge-based potential; decoy sets; ideal-gas reference state
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 10 11 nonhomologous (less than 30% homology) protein structures with resolution less than 2 Angstrom. 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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