Related papers: Derangement model of ligand-receptor binding
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of…
We devise a method for predicting certain receptor-ligand binding behaviors, based on stochastic dynamical modelling. We consider the dynamics of a receptor binding to a ligand on the cell membrane, where the receptor and ligand perform…
This comment is dedicated to the investigation of many-body localization in a quantum Ising model with long-range power law interactions, $r^{-\alpha}$, relevant for a variety of systems ranging from electrons in Anderson insulators to spin…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
A theoretical approach has been undertaken in order to model the thermodynamic equilibrium of a vesicle adhering to a flat substrate. The vesicle is treated in a canonical description with a fixed number of sites. A finite number of these…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
The entanglement can be localized between two noncomplementary parts of a many-body system by performing measurements on the rest of the system. This localized entanglement (LE) depends on the chosen basis set of measurement (BSM). We…
Predicting accurate protein-ligand binding affinity is important in drug discovery but remains a challenge even with computationally expensive biophysics-based energy scoring methods and state-of-the-art deep learning approaches. Despite…
In its vast majority entanglement verification is examined either in the complete characterized or totally device independent scenario. The assumptions imposed by these extreme cases are often either too weak or strong for real experiments.…
We determine the complete set of generalized spin squeezing inequalities. These are entanglement criteria that can be used for the experimental detection of entanglement in a system of spin-1/2 particles in which the spins cannot be…
We prove existence, uniqueness, and regularity for a reaction-diffusion system of coupled bulk-surface equations on a moving domain modelling receptor-ligand dynamics in cells. The nonlinear coupling between the three unknowns is through…
If only limited control over a multiparticle quantum system is available, a viable method to characterize correlations is to perform random measurements and consider the moments of the resulting probability distribution. We present…
Rebinding kinetics of molecular ligands plays a critical role in biomachinery, from regulatory networks to protein transcription, and is also a key factor for designing drugs and high-precision biosensors.In this study, we investigate…
A quantitative model of the mobility of functionalized particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles anchored through…
We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by…
We study entanglement dynamics in a diagonal dephasing model in which the strength of interaction decays exponentially with distance -- the so-called l-bit model of many-body localization. We calculate the exact expression for entanglement…
How cells reliably infer information about their environment is a fundamentally important question. While sensing and signaling generally start with cell-surface receptors, the degree of accuracy with which a cell can measure external…
The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…