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A reconstruction breaks down metabolic pathways (such as glycolysis and the citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
Pathway resources and types of pathway analysis using databases like KEGG, Reactome and WikiPathways. [1]Pathway is the term from molecular biology for a curated schematic representation of a well characterized segment of the molecular physiological machinery, such as a metabolic pathway describing an enzymatic process within a cell or tissue or a signaling pathway model representing a ...
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 ...
It is these sequences that are the so-called 'ancestors' – the process of synthesizing the corresponding DNA, transforming it into a cell and producing a protein is the so-called 'reconstruction'. Ancestral sequences are typically calculated by maximum likelihood, however Bayesian methods are also implemented. Because the ancestors are ...
The concept of ancestral reconstruction is often credited to Emile Zuckerkandl and Linus Pauling.Motivated by the development of techniques for determining the primary (amino acid) sequence of proteins by Frederick Sanger in 1955, [9] Zuckerkandl and Pauling postulated [10] that such sequences could be used to infer not only the phylogeny relating the observed protein sequences, but also the ...
Protein structure reconstruction refers to constructing an atomic-resolution model of a protein structure from incomplete coarse-grained representations [1] like, for example, protein contact maps, positions of alpha carbon atoms only or backbone chain atoms only.
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