Related papers: Exhaustive Search of Ligand Binding Pathways via V…

Metabolite structure identification has become the major bottleneck of the mass spectrometry based metabolomics research. Till now, number of mass spectra databases and search algorithms have been developed to address this issue. However,…

An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the…

Hydrodynamic interactions between particles confined in a liquid-filled linear channel are known to be screened beyond a distance comparable to the channel width. Using a simple analytical theory and lattice-Boltzmann simulations, we show…

The interpretation of ligand-target interactions at atomistic resolution is central to most efforts in computational drug discovery and optimization. However, the highly dynamic nature of protein targets, as well as possible induced fit…

The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…

Analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized…

The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…

Protein-ligand binding complexes are ubiquitous and essential to life. Protein-ligand binding affinity prediction (PLA) quantifies the binding strength between ligands and proteins, providing crucial insights for discovering and designing…

Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce…

Assessing drug-target affinity is a critical step in the drug discovery and development process, but to obtain such data experimentally is both time consuming and expensive. For this reason, computational methods for predicting binding…

The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…

Drug discovery represents a time-consuming and financially intensive process, and virtual screening can accelerate it. Scoring functions, as one of the tools guiding virtual screening, have their precision closely tied to screening…

Despite decades of advancements in automated ligand screening, large-scale drug discovery remains resource-intensive and requires post-processing hit selection, a step where chemists manually select a few promising molecules based on their…

Advances in controlled polymerization have enabled the synthesis of mechanically interlocked polymers like molecular knots and linear[n]catenane. These aesthetic macromolecules with unique topological constraints in the form of mechanical…

Using simulations, we construct the effective dynamics in metabasin space for a Lennard-Jones glass-former. Metabasins are identified via a scheme that measures transition rates between inherent structures, and generates clusters of…

Finding collective variables to describe some important coarse-grained information on physical systems, in particular metastable states, remains a key issue in molecular dynamics. Recently, machine learning techniques have been intensively…

Based on molecular dynamics simulations of a lithium metasilicate glass we study the potential of bond valence sum calculations to identify sites and diffusion pathways of mobile Li ions in a glassy silicate network. We find that the bond…

Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…

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…