Related papers: Predicting biomolecular binding kinetics: A review
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 understanding of how cells interact with their extracellular matrix via molecular bonds is fundamental for many important processes in cell biology and engineering. In these interactions, the deformability of cells and matrix…
Kinetic rate constants fundamentally characterize the dynamics of the chemical interaction of macromolecules, and thus their study sets a major direction in experimental biochemistry. The estimation of such constants is often challenging,…
We present a time-independent quantum formalism to describe the dynamics of molecules with permanent electric dipole moments in a two-dimensional confined geometry such as a one-dimensional optical lattice, in the presence of an electric…
Approximate molecular calculations via standard Kohn-Sham Density Functional Theory are exactly reproduced by performing self-consistent calculations on isolated fragments via Partition Density Functional Theory [Phys. Rev. A 82, 024501…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…
Recent advancements in protein docking site prediction have highlighted the limitations of traditional rigid docking algorithms, like PIPER, which often neglect critical stochastic elements such as solvent-induced fluctuations. These…
Current experimental and theoretical studies on the effect of intermolecular interactions on molecular conduction appear to be in conflict with each other. In particular, some experimental results, e.g., the observation of 2-dimensional…
The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes,…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
We present a novel machine learning approach to understanding conformation dynamics of biomolecules. The approach combines kernel-based techniques that are popular in the machine learning community with transfer operator theory for…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…
We propose a computational method to quantitatively evaluate the systematic uncertainties that arise from undetectable sources in biological measurements using live-cell imaging techniques. We then demonstrate this method in measuring…
Molecular docking, a key technique in structure-based drug design, plays pivotal roles in protein-ligand interaction modeling, hit identification and optimization, in which accurate prediction of protein-ligand binding mode is essential.…
The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…
Molecular dynamics (MD) simulations and computer-aided drug design (CADD) have advanced substantially over the past two decades, thanks to continuous computer hardware and software improvements. Given these advancements, MD simulations are…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Most machine learning models for materials science rely on descriptors based on materials compositions and structures, even though the chemical bond has been proven to be a valuable concept for predicting materials properties. Over the…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…