We introduce PyPE_RESP, a tool to facilitate and standardize partial atomic charge derivation using the RESP approach. PyPE_RESP builds upon open-source Python package RDKit for chemoinformatics AMBER suite molecular simulations. provides an easy setup of multi-conformer multi-molecule Re-strained Electrostatic Potential (RESP) fitting while allowing comprehensive definition constraint groups through multiple methods. As command line tool, can be integrated into batch processes. The software...

We introduce PyPE_RESP, a tool to facilitate and standardize partial atomic charge derivation using the Restrained Electrostatic Potential (RESP) approach. PyPE_RESP builds upon open-source Python package RDKit for chemoinformatics AMBER suite molecular simulations. provides an easy setup of multiconformer multimolecule RESP fitting while allowing comprehensive definition constraint groups through multiple methods. As command line tool, can be integrated into batch processes. The software...

Abstract Starch, a plant-derived insoluble carbohydrate composed of glucose polymers, is the principal in our diet and valuable raw material for industry. The properties starch depend on arrangement units within constituent polymers. However, key aspects structure underlying biosynthetic processes are not well understood, limiting progress towards targeted improvement crops. In particular, major component starch, amylopectin, has complex three-dimensional, branched architecture. This...

We study the effect of local regulation mechanisms on stochastic network traffic, based simple examples. Using totally asymmetric exclusion process a multiloop structure in which several segments share single junction, we illustrate mechanisms: (i) additional improve transport but saturates due to blockage, (ii) bias reduces overall and leads regimes, (iii) "pumping" particles out junctions, via locally increased hopping rate, allows us compensate bottlenecks becomes futile beyond...

During protein synthesis, charged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (aaRS). In humans, mutant aaRS cause a diversity of neurological disorders, but their molecular aetiologies incompletely characterised. To understand system responses depletion, the yeast glutamine gene (GLN4) was transcriptionally regulated using doxycycline tet-off control. Depletion Gln4p inhibited growth, induced GCN4 acid starvation response, indicative...

In humans, glycogen storage diseases result from metabolic inborn errors, and can lead to severe phenotypes lethal conditions. Besides these rare diseases, is also associated widely spread societal burdens such as diabetes. Glycogen a branched glucose polymer synthesised degraded by complex set of enzymes. Over the past 50 years, structure has been intensively investigated. Yet, interplay between detailed three-dimensional related enzyme activity only partially characterised still be fully...

ExpressInHost (<a href="https://gitlab.com/a.raguin/expressinhost" target="_blank">https://gitlab.com/a.raguin/expressinhost</a>) is a GTK/C++ based user friendly graphical interface that allows tuning the codon sequence of an mRNA for recombinant protein expression in host microorganism. Heterologous gene widely implemented biotechnology companies and academic research laboratories. However, proteins can be challenging. On one hand, maximising translation speed important, especially...

The processing of agricultural wastes towards extraction renewable resources is recently being considered as a promising alternative to conventional biofuel production. degradation residues complex chemical process that currently time intensive and costly. Various pre-treatment methods are investigated determine the subsequent modification material main obstacles in increasing enzymatic saccharification. In this study, we present computational model complements experimental approaches. We...

ABSTRACT During protein synthesis, charged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (aaRS). In humans, mutant aaRS cause a diversity of neurological disorders, but their molecular aetiologies incompletely characterised. To understand system responses depletion, the yeast glutamine gene ( GLN4 ) was transcriptionally regulated using doxycycline tet-off control. Depletion Gln4p inhibited growth, induced GCN4 acid starvation response,...

Corn stover is the most abundant form of crop residue that can serve as a source lignocellulosic biomass in biorefinery approaches, for instance production bioethanol. In such processes, constituent polysaccharide biopolymers are typically broken down into simple monomeric sugars by enzymatic saccharification, further downstream fermentation However, recalcitrance this material to saccharification invokes need innovative pre-treatment methods increase sugar conversion yield. Here, we focus...

Enzymatic digestion of lignocellulosic plant biomass is a key step in bio-refinery approaches for the production biofuels and other valuable chemicals. However, recalcitrance this material conjunction with its variability heterogeneity strongly hampers economic viability profitability biofuel production. To complement both academic industrial experimental research field, we designed an advanced web application that encapsulates our in-house developed complex biophysical model enzymatic cell...

Abstract In humans, glycogen storage diseases result from metabolic inborn errors, and can lead to severe phenotypes lethal conditions. Besides these rare diseases, is also associated widely spread societal burdens such as diabetes. Glycogen a branched glucose polymer synthesised degraded by complex set of enzymes. Over the past 50 years, structure has been intensively investigated. Yet, interplay between related enzymes still be characterised. this article, we develop stochastic...