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Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics andExpand
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Exploiting Enzyme Plasticity in Virtual Screening: High Efficiency Inhibitors of Glutamate Racemase.
Glutamate racemase is an attractive antimicrobial drug target. Virtual screening using a transition-state conformation of the enzyme resulted in the discovery of several μM competitive inhibitors,Expand
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Sequence Similarity Networks for the Protein Universe
As of November 2014, over 86 million protein sequences had been deposited in the TrEMBL database, of which only 0.5 million had experimental support for an enzymatic function. Currently, proteinExpand
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Nature of allosteric inhibition in glutamate racemase: discovery and characterization of a cryptic inhibitory pocket using atomistic MD simulations and pKa calculations.
Enzyme inhibition via allostery, in which the ligand binds remotely from the active site, is a poorly understood phenomenon and represents a significant challenge to structure-based drug design.Expand
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In silico Optimization of a Fragment‐Based Hit Yields Biologically Active, High‐Efficiency Inhibitors for Glutamate Racemase
A novel lead compound for inhibition of the antibacterial drug target, glutamate racemase (GR), was optimized for both ligand efficiency and lipophilic efficiency. A previously developed hybridExpand
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Biosynthesis of a Novel Glutamate Racemase Containing a Site-Specific 7-Hydroxycoumarin Amino Acid: Enzyme–Ligand Promiscuity Revealed at the Atomistic Level
Glutamate racemase (GR) catalyzes the cofactor independent stereoinversion of l- to d-glutamate for biosynthesis of bacterial cell walls. Because of its essential nature, this enzyme is under intenseExpand
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Flooding Enzymes: Quantifying the Contributions of Interstitial Water and Cavity Shape to Ligand Binding Using Extended Linear Response Free Energy Calculations
Glutamate racemase (GR) is a cofactor independent amino acid racemase that has recently garnered increasing attention as an antimicrobial drug target. There are numerous high resolution crystalExpand
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A Novel Pathway for Bacterial Ethanolamine Metabolism
Ethanolamine, a major component of the cell membranes of bacteria and animals in the form of phosphatidylethanolamine, can be a source of carbon and/or nitrogen for many bacterial species. The cano...
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