The molecular details involved in the folding, dynamics, organization, and interaction of
proteins with other molecules are often difficult to assess by experimental techniques …

Quercetin is a flavonoid with notable pharmacological effects and promising therapeutic
potential. Quercetin plays a significant role in neuroinflammation, which helps reduce …

Abstract Graphical Processor Units (GPUs) are nowadays widely used in all-atom molecular
simulations because of the advantage of efficient partitioning of atom pairs between the …

Abstract Summary The UNited RESisdue (UNRES) package for coarse-grained simulations,
which has recently been optimized to treat large protein systems, has been implemented on …

The influence of distance restraints from chemical cross-link mass spectroscopy (XL-MS) on
the quality of protein structures modeled with the coarse-grained UNRES force field was …

GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD)
software developed to simulate the conformational dynamics of a single biomolecule, as …

The dynamics of the virus like particles (VLPs) corresponding to the GII. 4 Houston, GII. 2
SMV, and GI. 1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis …

In this paper, we evaluated the ability of four coarse-grained methods to predict protein
flexible regions with potential biological importance, UNRES-flex, UNRES-DSSP-flex (based …

Heparin is an unbranched periodic polysaccharide composed of negatively charged
monomers and involved in key biological processes, including anticoagulation …

The association of 55 dipeptides extracted from aggregation-prone regions of selected
proteins was studied by means of multiplexed replica-exchange molecular dynamics …