Related papers: Predicting biomolecular binding kinetics: A review

In order to obtain a good understanding of astrochemistry, it is crucial to better understand the key parameters that govern grain-surface chemistry. For many chemical networks, these crucial parameters are the binding energies of the…

Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are…

Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between…

We show, through a machine learning approach, that the equilibrium distance, harmonic vibrational frequency, and binding energy of diatomic molecules are universally related. In particular, the relationships between spectroscopic constants…

Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…

The major histocompatibility complex (MHC) molecules, which bind peptides for presentation on the cell surface, play an important role in cell-mediated immunity. In light of developing databases and technologies over the years, significant…

Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…

Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins, either pre-existing or…

Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by…

Accurate prediction of molecular vibrational frequencies is important to identify spectroscopic signatures and reaction thermodynamics. In this work, we develop a method to quantify uncertainty associated with density functional theory…

Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…

In chemical crosslinking of gelatin solutions, two different time scales affect the kinetics of the gel formation in the experiments. We complement the experimental study with Monte Carlo numerical simulations of a lattice model. This…

We develop a model of molecular binding based on the Bohr-Sommerfeld description of atoms together with a constraint taken from conventional quantum mechanics. The model can describe the binding energy curves of H2, H3 and other molecules…

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…

Accurate prediction of drug-target binding affinity can accelerate drug discovery by prioritizing promising compounds before costly wet-lab screening. While deep learning has advanced this task, most models fuse ligand and protein…

Although atomistic simulations of proteins and other biological systems are approaching microsecond timescales, the quality of trajectories has remained difficult to assess. Such assessment is critical not only for establishing the…

Molecule representation learning is crucial for understanding and predicting molecular properties. However, conventional atom-centric models, which treat chemical bonds merely as pairwise interactions, often overlook complex bond-level…

The finite-frequency transport properties of a large-spin molecule attached to ferromagnetic contacts are studied theoretically in the Kondo regime. The focus is on the behavior of the dynamical conductance in the linear response regime,…

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…

We study the process of associating molecules from atomic gases using a magnetic field modulation that is resonant with the molecular binding energy. We show that maximal conversion is obtained by optimising the amplitude and frequency of…