Related papers: Comparative analysis of rigidity across protein fa…

A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes…

The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…

This work proposes a new efficient approach for calculating the bending stiffness of two-dimensional materials using simple atomistic tests on small periodic unit cells. The tests are designed such that bending deformations are dominating…

Accurate prediction of protein-protein binding affinity is vital for understanding molecular interactions and designing therapeutics. We adapt Boltz-2, a state-of-the-art structure-based protein-ligand affinity predictor, for…

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…

Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…

Proteins, by virtue of their central role in most biological processes, represent one of the key subjects of the study of molecular evolution. Inherent to the indispensability of proteins for living cells is the fact that a given protein…

Predicting the binding affinity of protein protein complexes directly from sequence remains a challenging problem, particularly in the absence of reliable structural information. Here I present ProtT Affinity, a sequence only model that…

This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…

We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…

We study the nature of the frictional jamming transition within the framework of rigidity percolation theory. Slowly sheared frictional packings are decomposed into rigid clusters and floppy regions with a generalization of the pebble game…

The role of heterogeneity in the plastic flow of thin ferrite specimens is investigated in this study. This is done through a recently introduced quasi-2D experimental-numerical framework that allows for a quantitative comparison of the…

Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…

Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…

We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…

A set of oxide and chalcogenide tetrahedral glasses are investigated using molecular dynamics simulations. It is shown that unlike stoichiometric selenides such as GeSe$_2$ and SiSe$_2$, germania and silica display large standard deviations…

Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…

Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…