When we used QSTS in the MLM model, the probability plot was much closer to the diagonal, suggesting that the correction for the structure was much better, and thus we present the associations obtained with this model with corrected P values less than 0.05 (Table 2).
The immune-related pathways 'Human Cytomegalovirus and Map Kinase Pathways', 'The information-processing pathway at the Interferon-beta enhancer', 'T Cell Receptor Signaling Pathway' and 'Toll-Like Receptor Pathway' are enriched in the original model (all with corrected P < 0.05) but not the no-RNAi SDREM model.
Here, we propose a method to design simplified models with correct voltage attenuation, based on camera-lucida reconstructions of neurons.
Similarly to GLS, GEE produces marginal models with correct SE estimates and inferences.
The interacting regions were analysed only for dimer models with correct orientation in the membrane (N-in and C-out for both protomers).
100 outputs were generated and the dimer models, with correct membrane orientation and low energy, were chosen for analysis of regions that form the interface.
In the context of protein model assessment, two types of baseline values are of interest: the expected score when comparing two random structures, and scores for models with correct folds but including threading errors.
Currently, no other approach is able to generate complete pathway models with correct reactions, including stoichiometry and well-annotated SBML (i.e., including SBO terms or MIRIAM URNs) or valid BioPAX documents.
Out of the 5 to 10 different structures submitted by each participating modeling team for each puzzle, we and others have been unable to rank the models with correct tertiary helical arrangements as our top submissions, much less confidently assign accuracies to these models or select candidates for computationally expensive refinement.
Final models with correct folds (TM-score >0.5) were obtained by further I-TASSER refinements for proteins of more than 150 residues, an unprecedented success in terms of the size of the successfully folded proteins in Free Modeling in the CASP experiment.
