Related papers: Soft disorder modulates the assembly path of prote…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change…
Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study aggregation of short peptides in a coarse-grained model with…
The main objective of this work is to numerically investigate the effect of geometric imperfections on the macroscopic response and domain formation in soft biological composites that exhibit plasticity in the stiff (fiber) phase.This work…
Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…
AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step…
Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…
We simulate binary soft disk systems in two dimensions, and investigate how the dynamics slow as the area fraction is increased toward the glass transition. The "fragility" quantifies how sensitively the relaxation time scale depends on the…
What are the structural determinants of protein sequence evolution? A number of site-specific structural characteristics have been proposed, most of which are broadly related to either the density of contacts or the solvent accessibility of…
Soft composite solids, comprising discrete inclusions embedded within a compliant matrix, are emerging candidates for engineering synthetic tissues and soft robotic materials. Current strategies for controlling their nonlinear mechanics,…
The effect of increasing structural disorder on the distribution of contact forces P(f), inside three dimensional particle assemblies is systematically studied using computer simulations of model granular packings. Starting from a…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
Natural materials often feature a combination of soft and stiff phases, arranged to achieve excellent mechanical properties, such as high strength and toughness. Many natural materials have even independently evolved to have similar…
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…
Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…
Confinement can significantly alter fluid properties, offering potential for specific technological applications. However, achieving precise control over the structural complexity of confined fluids and soft matter remains challenging, as…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
The method of Probability Density Profile Analysis has been introduced previously as a tool to find the best match between a set of experimentally generated Residual Dipolar Couplings and a set of known protein structures. While it proved…