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Analyses on hydrophobicity and attractiveness of all‐atom distance‐dependent potentials
Author(s) -
Shirota Matsuyuki,
Ishida Takashi,
Kinoshita Kengo
Publication year - 2009
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 - 10.1002/pro.201
Subject(s) - atom (system on chip) , attractiveness , correlation , measure (data warehouse) , chemistry , statistical physics , chemical physics , atomic physics , biological system , physics , computer science , data mining , mathematics , biology , psychology , geometry , psychoanalysis , embedded system
Abstract Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states , have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all‐atom distance‐dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT‐TS score, but decreased the Z ‐score of the native structure. The attractiveness of potential improved both the correlation and Z ‐score for template‐based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states.