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More recently, the term MQAP (model quality assessment program) has been introduced to refer, generally, to the class of methods aimed at the ranking of structures within a given set of candidate models.
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For ranking of the structures we considered only the first block of an InChiKey to discard enantiomeric or diastereomeric isomers.
In addition to the already mentioned VS metrics, Additional file 2 contains the complete ranking of all structures and several VS metrics for each method and data set.
The network parameters from the PSNs are combined with SVM to build a mathematical model and the ranking of each structure is determined using logistic regression analysis.
While chemical mapping constraints do not improve the predicted minimum free energy structure, they do eliminate many possible structures and raise the rank of a structure that is 93.2% accurate (Table 1).
Additionally, there are doubts about the ability of docking approaches to predict the affinity or even the rank of the structures [6].
Although relative abundance cutoffs were used to filter out noisy data, ion abundances were not used by MS-FINDER for calculation of either the score or rank of candidate structures.
Initial ranking of the host structures is based on how well bond vectors on the donor groups match bond vectors on the linkages.
Second phase: the second phase outputs the final ranking of the generated structures in the first phase corresponding to the mass peak.
The economic penalty associated with the variability of main process variables close to active constraints is used in this work in order to develop a quantitative measure for the ranking of alternative control structures.
Extensive efforts have been made to enhance the conformational sampling (Das and Baker 2007; Frellsen et al. 2009) and to establish accurate scoring functions for the ranking of the different structures (Ding et al. 2008; Parisien and Major 2008).
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