The Role of Independent Test Set in Modeling of Protein Folding Kinetics

Author(s):  
Nikola Štambuk ◽  
Paško Konjevoda
2006 ◽  
Vol 15 (3) ◽  
pp. 564-582 ◽  
Author(s):  
Paul A. Ellison ◽  
Silvia Cavagnero

Structure ◽  
2004 ◽  
Vol 12 (10) ◽  
pp. 1833-1845 ◽  
Author(s):  
Suhail A. Islam ◽  
Martin Karplus ◽  
David L. Weaver

2020 ◽  
Author(s):  
Adam J. Hockenberry ◽  
Claus O. Wilke

AbstractMotivationBacteriophages are broadly classified into two distinct lifestyles: temperate (lysogenic) and virulent (lytic). Temperate phages are capable of a latent phase of infection within a host cell, whereas virulent phages directly replicate and lyse host cells upon infection. Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution.ResultsHere, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier. The classifier was trained on 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98%, greatly exceeding that of the best existing available tool (79%).AvailabilityBACPHLIP is freely available on GitHub (https://github.com/adamhockenberry/bacphlip) and the code used to build and test the classifier is provided in a separate repository (https://github.com/adamhockenberry/bacphlip-model-dev).


2006 ◽  
Vol 323 (1) ◽  
pp. 66-77 ◽  
Author(s):  
Young Min Rhee ◽  
Vijay S. Pande

1990 ◽  
Vol 29 (03) ◽  
pp. 167-181 ◽  
Author(s):  
G. Hripcsak

AbstractA connectionist model for decision support was constructed out of several back-propagation modules. Manifestations serve as input to the model; they may be real-valued, and the confidence in their measurement may be specified. The model produces as its output the posterior probability of disease. The model was trained on 1,000 cases taken from a simulated underlying population with three conditionally independent manifestations. The first manifestation had a linear relationship between value and posterior probability of disease, the second had a stepped relationship, and the third was normally distributed. An independent test set of 30,000 cases showed that the model was better able to estimate the posterior probability of disease (the standard deviation of residuals was 0.046, with a 95% confidence interval of 0.046-0.047) than a model constructed using logistic regression (with a standard deviation of residuals of 0.062, with a 95% confidence interval of 0.062-0.063). The model fitted the normal and stepped manifestations better than the linear one. It accommodated intermediate levels of confidence well.


1981 ◽  
Vol 5 (2) ◽  
pp. 92-96 ◽  
Author(s):  
James L. Smith ◽  
Roy A. Mead

Abstract Two aerial photo volume prediction models, Avery's Composite Aerial Volume Table, and Mead's Quadratic Model, were compared using graphs and a small independent test set. The graphs indicated that Mead's model predicted higher merchantable volumes for pine stands in central Mississippi than did Avery's model. Both models tended to underpredict ground merchantable volume. However, only Avery's model underpredicted in a statistically significant manner. Even though the possibility of negative volume predictions exists when using Mead's Quadratic Model, it was deemed the superior model of the two investigated.


2013 ◽  
Vol 4 (6) ◽  
pp. 597-604 ◽  
Author(s):  
Yuji Hidaka ◽  
Shigeru Shimamoto

AbstractDisulfide-containing proteins are ideal models for studies of protein folding as the folding intermediates can be observed, trapped, and separated by HPLC during the folding reaction. However, regulating or analyzing the structures of folding intermediates of peptides and proteins continues to be a difficult problem. Recently, the development of several techniques in peptide chemistry and biotechnology has resulted in the availability of some powerful tools for studying protein folding in the context of the structural analysis of native, mutant proteins, and folding intermediates. In this review, recent developments in the field of disulfide-coupled peptide and protein folding are discussed, from the viewpoint of chemical and biotechnological methods, such as analytical methods for the detection of disulfide pairings, chemical methods for disulfide bond formation between the defined Cys residues, and applications of diselenide bonds for the regulation of disulfide-coupled peptide and protein folding.


1993 ◽  
Vol 90 (5) ◽  
pp. 1942-1946 ◽  
Author(s):  
K. A. Dill ◽  
K. M. Fiebig ◽  
H. S. Chan

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