Dataset Information

MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials.

ABSTRACT:

Background

Protein model quality assessment (QA) is an essential procedure in protein structure prediction. QA methods can predict the qualities of protein models and identify good models from decoys. Clustering-based methods need a certain number of models as input. However, if a pool of models are not available, methods that only need a single model as input are indispensable.

Results

We developed MASS, a QA method to predict the global qualities of individual protein models using random forests and various novel energy functions. We designed six novel energy functions or statistical potentials that can capture the structural characteristics of a protein model, which can also be used in other protein-related bioinformatics research. MASS potentials demonstrated higher importance than the energy functions of RWplus, GOAP, DFIRE and Rosetta when the scores they generated are used as machine learning features. MASS outperforms almost all of the four CASP11 top-performing single-model methods for global quality assessment in terms of all of the four evaluation criteria officially used by CASP, which measure the abilities to assign relative and absolute scores, identify the best model from decoys, and distinguish between good and bad models. MASS has also achieved comparable performances with the leading QA methods in CASP12 and CASP13.

Conclusions

MASS and the source code for all MASS potentials are publicly available at http://dna.cs.miami.edu/MASS/ .

SUBMITTER: Liu T

PROVIDER: S-EPMC7336608 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials.

Liu Tong T Wang Zheng Z

BMC bioinformatics 20200706 Suppl 4

<h4>Background</h4>Protein model quality assessment (QA) is an essential procedure in protein structure prediction. QA methods can predict the qualities of protein models and identify good models from decoys. Clustering-based methods need a certain number of models as input. However, if a pool of models are not available, methods that only need a single model as input are indispensable.<h4>Results</h4>We developed MASS, a QA method to predict the global qualities of individual protein models usi ...[more]

PMID: 32631256

Similar Datasets

Project description:A central assumption in the behavioral sciences is that choice behavior generalizes enough across individuals that measurements from a sampled group can predict the behavior of the population. Following from this assumption, the unit of behavioral sampling or measurement for most neuroimaging studies is the individual; however, cognitive neuroscience is increasingly acknowledging a dissociation between neural activity that predicts individual behavior and that which predicts the average or aggregate behavior of the population suggesting a greater importance of individual differences than is typically acknowledged. For instance, past work has demonstrated that some, but not all, of the neural activity observed during value-based decision-making is able to predict not just individual subjects' choices but also the success of products on large, online marketplaces-even when those two behavioral outcomes deviate from one another-suggesting that some neural component processes of decision-making generalize to aggregate market responses more readily across individuals than others do. While the bulk of such research has highlighted affect-related neural responses (i.e. in the nucleus accumbens) as a better predictor of group-level behavior than frontal cortical activity associated with the integration of more idiosyncratic choice components, more recent evidence has implicated responses in visual cortical regions as strong predictors of group preference. Taken together, these findings suggest a role of neural responses during early perception in reinforcing choice consistency across individuals and raise fundamental scientific questions about the role sensory systems in value-based decision-making processes. We use a multivariate pattern analysis approach to show that single-trial visually evoked electroencephalographic (EEG) activity can predict individual choice throughout the post-stimulus epoch; however, a nominally sparser set of activity predicts the aggregate behavior of the population. These findings support an account in which a subset of the neural activity underlying individual choice processes can scale to predict behavioral consistency across people, even when the choice behavior of the sample does not match the aggregate behavior of the population.

Project description:ObjectiveTo predict a woman's risk of postpartum hemorrhage at labor admission using machine learning and statistical models.MethodsPredictive models were constructed and compared using data from 10 of 12 sites in the U.S. Consortium for Safe Labor Study (2002-2008) that consistently reported estimated blood loss at delivery. The outcome was postpartum hemorrhage, defined as an estimated blood loss at least 1,000 mL. Fifty-five candidate risk factors routinely available on labor admission were considered. We used logistic regression with and without lasso regularization (lasso regression) as the two statistical models, and random forest and extreme gradient boosting as the two machine learning models to predict postpartum hemorrhage. Model performance was measured by C statistics (ie, concordance index), calibration, and decision curves. Models were constructed from the first phase (2002-2006) and externally validated (ie, temporally) in the second phase (2007-2008). Further validation was performed combining both temporal and site-specific validation.ResultsOf the 152,279 assessed births, 7,279 (4.8%, 95% CI 4.7-4.9) had postpartum hemorrhage. All models had good-to-excellent discrimination. The extreme gradient boosting model had the best discriminative ability to predict postpartum hemorrhage (C statistic: 0.93; 95% CI 0.92-0.93), followed by random forest (C statistic: 0.92; 95% CI 0.91-0.92). The lasso regression model (C statistic: 0.87; 95% CI 0.86-0.88) and logistic regression (C statistic: 0.87; 95% CI 0.86-0.87) had lower-but-good discriminative ability. The above results held with validation across both time and sites. Decision curve analysis demonstrated that, although all models provided superior net benefit when clinical decision thresholds were between 0% and 80% predicted risk, the extreme gradient boosting model provided the greatest net benefit.ConclusionPostpartum hemorrhage on labor admission can be predicted with excellent discriminative ability using machine learning and statistical models. Further clinical application is needed, which may assist health care providers to be prepared and triage at-risk women.

Dataset Information

MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials.

Background

Results

Conclusions

Publications

MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets