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Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Recent studies reported that adenosine triphosphate (ATP) could inhibit as well as enhance the phase separation in prion-like proteins. The molecular mechanism underlying such a puzzling phenomenon remains elusive. Here, taking the fused in…
Emergence of collective dynamical chirality (CDC) at mesoscopic scales plays a key role in many formation processes of chiral structures in nature, which may also provide possible routines for people to fabricate complex chiral…
The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with…
The global pandemic due to emergence of COVID 19 has created the unrivaled public health crisis. It has huge morbidity rate never comprehended in the recent decades. Researchers have made many efforts to find the optimal solution of this…
The bioprotective nature of disaccharides is hypothesized to derive from the modification of the hydrogen bonding network of water which protects biomolecules through lowered water activity at the protein interface. Using ultrafast…
The mobility of water molecules confined in a silica pore is studied by computer simulation in the low hydration regime, where most of the molecules reside close to the hydrophilic substrate. A layer analysis of the single particle dynamics…
This paper introduces several proof-of-concept (PoC) computational methods intended to offer biochemical researchers straightforward, time- and cost-effective strategies to accelerate their work. While Machine Learning (ML) models were…
Nearly a quarter of genomic sequences and almost half of all receptors that are likely to be targets for drug design are integral membrane proteins. Understanding the detailed mechanisms of the folding of membrane proteins is a largely…
How molecular motors like Kinesin regulates the affinity to the rail protein in the process of ATP hydrolysis remains to be uncovered. To understand the regulation mechanism, we investigate the structural fluctuation of KIF1A in different…
The quasi-equilibrium approximation is acceptable when molecular interactions are fast enough compared to circuit dynamics, but is no longer allowed when cellular activities are governed by rare events. A typical example is the lactose…
Despite continuing hype about the role of AI in drug discovery, no "AI-discovered drugs" have so far received regulatory approval. Here we assess one of the latest AI based tools in this domain. The ability to rapidly predict protein-ligand…
Using molecular dynamics simulations we study the slow dynamics of a colloidal fluid annealed within a matrix of obstacles quenched from an equilibrated colloidal fluid. We choose all particles to be of the same size and to interact as hard…
Using coarse-grained molecular dynamics simulations, we analyze mechanically induced dissociation and unfolding of the protein complex CD48-2B4. This heterodimer is an indispensable component of the immunological system: 2B4 is a receptor…
By using event-driven molecular dynamics simulation, we investigate effects of varying the area fraction of the smaller component on structure, compressibility factor and dynamics of the highly size-asymmetric binary hard-disk liquids. We…
To overcome antimalarial drug resistance, carbohydrate derivatives as selective PfHT1 inhibitor have been suggested in recent experimental work with orthosteric and allosteric dual binding pockets. Inspired by this promising therapeutic…
Active gels made of cytoskeletal proteins are valuable materials with attractive non-equilibrium properties such as spatial self-organization and self-propulsion. At least four typical routes to spatial patterning have been reported to date…
The synthesis of the high-$T_c$ superhydride CaH$_6$ has stimulated significant interest in understanding synthesis pathways for metastable hydrides. However, the microscopic mechanisms governing such hydrogenation reactions remain poorly…
The dynamics of many macromolecular machines is characterized by chemically-mediated structural changes that achieve large scale functional deployment through local rearrangements of constitutive protein sub-units. Motivated by recent high…
Active droplets are artificial microswimmers built from a liquid dispersion by microfluidic tools and showing self-propelled motion. These systems hold particular interest for mimicking biological phenomena, such as some aspects of cell…