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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-dimensional (3D) metabolite andExpand
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iML1515, a knowledgebase that computes Escherichia coli traits
iML1515, a knowledgebase that computes Escherichia coli traits To the Editor: Extracting knowledge from the many types of big data produced by high-throughput methods remains a challenge, even whenExpand
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Antigen receptor repertoire profiling from RNA-seq data
VOLUME 35 NUMBER 10 OCTOBER 2017 NATURE BIOTECHNOLOGY 24. Schellenberger, J. et al. Nat. Protoc. 6, 1290–1307 (2011). 25. Guzmán, G.I. et al. Proc. Natl. Acad. Sci. USA 112, 929–934 (2015). 26.Expand
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Model-driven discovery of underground metabolic functions in Escherichia coli
Significance Organisms have evolved to take advantage of their environment. Enzymes drive this adaptability by displaying flexibility in terms of substrate specificity and catalytic promiscuity. ThisExpand
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Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States.
The current state of the art of Quantum Mechanical/molecular mechanical (QM/MM) molecular dynamics approaches in ground and electronically excited states and their applications to biological problemsExpand
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Integrating computational methods to retrofit enzymes to synthetic pathways
Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilizeExpand
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Recon3D: A Resource Enabling 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-dimensional (3D) metabolite andExpand
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Directed evolution of the suicide protein O⁶-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability.
Here we present a biophysical, structural, and computational analysis of the directed evolution of the human DNA repair protein O(6)-alkylguanine-DNA alkyltransferase (hAGT) into SNAP-tag, aExpand
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Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.
Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present aExpand
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Systems biology of the structural proteome
BackgroundThe success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on anExpand
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