Related papers: Estimation of protein folding probability from equ…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…
Background:Prediction of protein three-dimensional structures from amino acid sequences is a long-standing goal in computational/molecular biology. The successful discrimination of protein folds would help to improve the accuracy of protein…
Most of the current understanding of structure-property relations at the molecular and the supramolecular scales can be formulated in terms of the stability of and the interactions between a limited number of recurring structural motifs…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
We develop a unified scaling framework for the end-position distributions of tethered polymers confined in finite cylindrical geometries. Two observables are analysed: the longitudinal distribution P(x), along the confinement axis, and the…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differences) depend on the relative populations of different…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
A probabilistic clustering algorithm is proposed for the analysis of forensic DNA mixtures in which individual cells are isolated and short tandem repeats are amplified using the polymerase chain reaction to generate single cell…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
Folding is emerging as a promising manufacturing process to transform flat materials into functional structures, offering efficiency by reducing the need for welding, gluing, and molding, while minimizing waste and enabling automation.…
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica…
Protein folding produces characteristic and functional three-dimensional structures from unfolded polypeptides or disordered coils. The emergence of extraordinary complexity in the protein folding process poses astonishing challenges to…
Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying…
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…
A method for reconstructing the energy landscape of simple polypeptidic chains is described. We show that we can construct an equivalent representation of the energy landscape by a suitable directed graph. Its topological and dynamical…
To explain the observed dynamics in equilibrium single-molecule measurements of biomolecules, the experimental observable is often chosen as a putative reaction coordinate along which kinetic behavior is presumed to be governed by diffusive…