Current status and applications of genome-scale metabolic models
Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …
associations for entire metabolic genes in an organism, and can be simulated to predict …
Reconstructing organisms in silico: genome-scale models and their emerging applications
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …
of published studies detailing its genes, its genome and the biochemical functions of its …
The RCSB protein data bank: integrative view of protein, gene and 3D structural information
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB, http://rcsb. org), the US data center for the global PDB archive, makes PDB data freely …
PDB, http://rcsb. org), the US data center for the global PDB archive, makes PDB data freely …
Recon3D enables a three-dimensional view of gene variation in human metabolism
Genome-scale network reconstructions have helped uncover the molecular basis of
metabolism. Here we present Recon3D, a computational resource that includes three …
metabolism. Here we present Recon3D, a computational resource that includes three …
iML1515, a knowledgebase that computes Escherichia coli traits
Figure 1 iML1515 genome-scale reconstruction.(a) The iML1515 model contains 1,515
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
open reading frames that encode enzymes that catalyze 2,719 reactions involving 1,192 …
A map of protein-metabolite interactions reveals principles of chemical communication
Metabolite-protein interactions control a variety of cellular processes, thereby playing a
major role in maintaining cellular homeostasis. Metabolites comprise the largest fraction of …
major role in maintaining cellular homeostasis. Metabolites comprise the largest fraction of …
Antigen receptor repertoire profiling from RNA-seq data
To the Editor: Somatic recombination and accumulation of mutations in VDJ segments result
in vast heterogeneity of T-cell receptor (TCR) and immunoglobulin repertoires1, 2. High …
in vast heterogeneity of T-cell receptor (TCR) and immunoglobulin repertoires1, 2. High …
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education
Abstract The Protein Data Bank (PDB) is one of two archival resources for experimental data
central to biomedical research and education worldwide (the other key Primary Data Archive …
central to biomedical research and education worldwide (the other key Primary Data Archive …
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
Knowing the catalytic turnover numbers of enzymes is essential for understanding the
growth rate, proteome composition, and physiology of organisms, but experimental data on …
growth rate, proteome composition, and physiology of organisms, but experimental data on …
Machine learning for the advancement of genome-scale metabolic modeling
Constraint-based modeling (CBM) has evolved as the core systems biology tool to map the
interrelations between genotype, phenotype, and external environment. The recent …
interrelations between genotype, phenotype, and external environment. The recent …