Park and Levitt decoys

Figure 1. OPLS-AA/SGB Energy gap/RMS correlation plots for the Park and Levitt decoy...

Gap, min (A /), and the RMS Devition Between the Best-Scoring Decoy and the Native Conformation the Native Z-Score Z at and the Average Z-Score Znat-me of the Native-like Conformations of the Park and Levitt Decoy Sets [60]... 

Figure 2. Fraction of the Park and Levitt decoys with energy gap from the native less than AI/ which are native-like (RMSD from native <3 A), using the OPLS-AA/SGB potential function and the vacuum OPLS-AA potential with screened Coulomb interactions.

Figure 4. The distribution of energy gaps from the native for the 3icb data set of the Park and Levitt decoys using various energy functions.

Figure 8. Distributioii of energy gaps from the native of the 3icb Park and Levitt decoys for the total OPLS-AA/SGB energy and for the van der Waals, f/vdw. intramolecular Coulomb, f/coniomb. and solvation, Usgb, energy components.

Ithough knowledge-based potentials are most popular, it is also possible to use other types potential function. Some of these are more firmly rooted in the fundamental physics of iteratomic interactions whereas others do not necessarily have any physical interpretation all but are able to discriminate the correct fold from decoy structures. These decoy ructures are generated so as to satisfy the basic principles of protein structure such as a ose-packed, hydrophobic core [Park and Levitt 1996]. The fold library is also clearly nportant in threading. For practical purposes the library should obviously not be too irge, but it should be as representative of the different protein folds as possible. To erive a fold database one would typically first use a relatively fast sequence comparison lethod in conjunction with cluster analysis to identify families of homologues, which are ssumed to have the same fold. A sequence identity threshold of about 30% is commonly... 

Park and Levitt [60] have evaluated six simple empirical scoring functions using the same decoy sets examined in this work. A comparison between the native and native-like Z scores calculated here with those obtained by Park and Levitt shows that the OPLS-AA/SGB energy model clearly outperforms the six empirical scoring functions examined in the Park and Levitt work. Moreover, none of the empirical scoring functions examined by Park and Levitt was able to consistently rank first the native conformation, whereas the OPLS/SGB model does. 

Figure 9. Near-native and non-native distributions of the OPLS-AA/SGB and van der Waals energy gaps ftom the native for the Park and Levitt 3icb decoys.

Park B and M Levitt 1996. Energy Functions that Discriminate X-ray and Near-native Folds from V constructed Decoys, journal of Molecular Biology 258 367-392. 

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