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Fold (major structural similarity): Proteins are defined as having a common fold if they have the same major secondary structures in the same arrangement and with the same topological connections. Different proteins with the same fold often have peripheral elements of secondary structure and turn regions that differ in size and conformation.
This type of method is also known as 3D-1D fold recognition due to its compatibility analysis between three-dimensional structures and linear protein sequences. This method has also given rise to methods performing an inverse folding search by evaluating the compatibility of a given structure with a large database of sequences, thus predicting ...
The term "ultra-deep" can sometimes also refer to higher coverage (>100-fold), which allows for detection of sequence variants in mixed populations. [ 5 ] [ 6 ] [ 7 ] In the extreme, error-corrected sequencing approaches such as Maximum-Depth Sequencing can make it so that coverage of a given region approaches the throughput of a sequencing ...
Schematic overview of the modular structure underlying procedures for gene set enrichment analysis. Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g ...
When the limbs of a fold converge upward, the fold is referred to as an antiform. Conversely, when the limbs of a fold converge downward, the fold is known as a synform. Not to be confused with these terms (antiform and synform), the terms anticline and syncline are used in the description of the stratigraphic significance of the fold.
The diagram sketches how proteins fold into their native structures by minimizing their free energy. The folding funnel hypothesis is a specific version of the energy landscape theory of protein folding, which assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells.
In structural geology, a syncline is a fold with younger layers closer to the center of the structure, whereas an anticline is the inverse of a syncline. A synclinorium (plural synclinoriums or synclinoria ) is a large syncline with superimposed smaller folds. [ 1 ]
This plot is colored such that those points having a fold-change less than 2 (log 2 = 1) are shown in gray. In statistics, a volcano plot is a type of scatter-plot that is used to quickly identify changes in large data sets composed of replicate data. [1] [2] It plots significance versus fold-change on the y and x axes