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Nature has generated an impressive set of proteins with diverse folds and functions.
The term carbohydrate-recognition domain is often used as a general label that encompasses all of the diverse folds, functions and sites of expression.
The confusion matrices for LP, SVM, and Lasso prediction models are provided in Additional File 2. For k-fold cross validation across sequentially diverse folds, we report the accuracy and MCC values for k = 19, 30, 50, 70 in Table 5.
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The Cupin superfamily was identified by Dunwell in 1998 [ 7] and is among the most functionally diverse folding described to date, comprising both enzymatic and non-enzymatic members.
Their larger size should theoretically afford the ability to generate more diverse folding patterns, skeletal rearrangements, and tailoring modifications than is seen in the biosynthesis of the smaller aromatic PKs.
Several diverse protein folds are currently under development on the basis of modular construction, a strategy also observed in families of naturally evolved immune receptors.
Over the past 20 years, however, they have emerged as one of the most diverse protein folds in nature, enabling many biological functions beyond mechanical rigidity, such as membrane fusion, signal transduction, and solute transport.
However, these diverse sequences fold to adopt a common three dimensional structure with two conserved elements: (i) the PxxP motif capable of interacting with SH3 domain; (ii) the basic residues that constitute the PI binding pocket [ 10].
The mammalian endoplasmic reticulum (ER) contains a diverse oxidative protein folding network in which ERp46, a member of the protein disulfide isomerase (PDI) family, serves as an efficient disulfide bond introducer together with Peroxiredoxin-4 (Prx4).
We selected genes with a diverse range of fold change (from 1.3 to 7) for our validation studies using qRT-PCR.
Hydrogen/deuterium exchange (HDX) with mass spectrometry (MS) detection has evolved in the past two decades into a powerful tool that is now used to decipher intimate details of processes as diverse as protein folding, recognition and binding, and enzyme catalysis.
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