Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling

L Zhao, HL Ciallella, LM Aleksunes, H Zhu - Drug discovery today, 2020 - Elsevier
Highlights•Drug discovery has been advanced to a big data era with a large amount of
public data sources available.•Ten V features (volume, velocity, variety, veracity, validity …

Escherichia coli as a host for metabolic engineering

S Pontrelli, TY Chiu, EI Lan, FYH Chen, P Chang… - Metabolic …, 2018 - Elsevier
Over the past century, Escherichia coli has become one of the best studied organisms on
earth. Features such as genetic tractability, favorable growth conditions, well characterized …

[HTML][HTML] Investigating mitochondrial redox state using NADH and NADPH autofluorescence

TS Blacker, MR Duchen - Free Radical Biology and Medicine, 2016 - Elsevier
The redox states of the NAD and NADP pyridine nucleotide pools play critical roles in
defining the activity of energy producing pathways, in driving oxidative stress and in …

Separating NADH and NADPH fluorescence in live cells and tissues using FLIM

TS Blacker, ZF Mann, JE Gale, M Ziegler… - Nature …, 2014 - nature.com
NAD is a key determinant of cellular energy metabolism. In contrast, its phosphorylated form,
NADP, plays a central role in biosynthetic pathways and antioxidant defence. The reduced …

Glycolytic strategy as a tradeoff between energy yield and protein cost

A Flamholz, E Noor, A Bar-Even… - Proceedings of the …, 2013 - National Acad Sciences
Contrary to the textbook portrayal of glycolysis as a single pathway conserved across all
domains of life, not all sugar-consuming organisms use the canonical Embden–Meyerhoff …

eQuilibrator—the biochemical thermodynamics calculator

A Flamholz, E Noor, A Bar-Even… - Nucleic acids research, 2012 - academic.oup.com
The laws of thermodynamics constrain the action of biochemical systems. However,
thermodynamic data on biochemical compounds can be difficult to find and is cumbersome …

Emergence of robust growth laws from optimal regulation of ribosome synthesis

M Scott, S Klumpp, EM Mateescu… - Molecular systems biology, 2014 - embopress.org
Bacteria must constantly adapt their growth to changes in nutrient availability; yet despite
large‐scale changes in protein expression associated with sensing, adaptation, and …

Transformation of biomass into commodity chemicals using enzymes or cells

AJJ Straathof - Chemical reviews, 2014 - ACS Publications
Biomass can be classified broadly as all the matter on the earth's surface of recent biological
origin. 1 Biomass includes plant materials such as trees, grasses, agricultural crops, algal …

[HTML][HTML] The BRENDA enzyme information system–From a database to an expert system

I Schomburg, L Jeske, M Ulbrich, S Placzek… - Journal of …, 2017 - Elsevier
Enzymes, representing the largest and by far most complex group of proteins, play an
essential role in all processes of life, including metabolism, gene expression, cell division …

How fast‐growing bacteria robustly tune their ribosome concentration to approximate growth‐rate maximization

E Bosdriesz, D Molenaar, B Teusink… - The FEBS …, 2015 - Wiley Online Library
Maximization of growth rate is an important fitness strategy for bacteria. Bacteria can achieve
this by expressing proteins at optimal concentrations, such that resources are not wasted …