title: Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction.
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.
authors.affiliation: Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology & Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA.
authors.forename: Hongyi
authors.initials: H
authors.lastname: Zhou
authors.forename: Yaoqi
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D019295:Computational Biology; D008433:Mathematics; D008962:Models, Theoretical; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013223:Statistics as Topic; D013816:Thermodynamics
chemical_list: D011506:Proteins