OBJECTIVES: In recent clinical studies, saxagliptin exhibited nephroprotective potential by lowering albuminuria. In this study, we aimed to determine whether these kidney effects of saxagliptin were mediated by changes in markers of kidney tubular d...
Journal of chemical theory and computation
30550274
Accurate force fields are crucial for molecular dynamics investigation of complex biological systems. Building accurate protein force fields from quantum mechanical (QM) calculations is challenging due to the complexity of proteins and high computati...
Computational and mathematical methods in medicine
33029195
Heat shock proteins (HSPs) are ubiquitous in living organisms. HSPs are an essential component for cell growth and survival; the main function of HSPs is controlling the folding and unfolding process of proteins. According to molecular function and m...
Biochimica et biophysica acta. General subjects
32298789
BACKGROUND: Compared with all-atom molecular dynamics (MD), constrained MD methods allow for larger time steps, potentially reducing computational cost. For this reason, there has been continued interest in improving constrained MD algorithms to incr...
Recurrent neural networks have led to breakthroughs in natural language processing and speech recognition. Here we show that recurrent networks, specifically long short-term memory networks can also capture the temporal evolution of chemical/biophysi...
International journal of biological macromolecules
33212104
Small heat shock protein (sHSP) is a superfamily of molecular chaperone and is found from archaea to human. Recent researches have demonstrated that sHSPs participate in a series of biological processes and are even closely associated with serious di...
Journal of chemical theory and computation
33662202
With the continual improvement of computing hardware and algorithms, simulations have become a powerful tool for understanding all sorts of (bio)molecular processes. To handle the large simulation data sets and to accelerate slow, activated transitio...
BACKGROUND: Antifreeze proteins (AFPs) are a group of proteins that inhibit body fluids from growing to ice crystals and thus improve biological antifreeze ability. It is vital to the survival of living organisms in extremely cold environments. Howev...
A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing the product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates usi...
Identification of ubiquitination sites is central to many biological experiments. Ubiquitination is a kind of post-translational protein modification (PTM). It is a key mechanism for increasing protein diversity and plays a vital role in regulating c...