The characterization of the 3D structure of oligosaccharides, their conjugates and analogs is
particularly challenging for traditional experimental methods. Molecular simulation methods …

The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and
molecular biology that requires a new paradigm to connect structural disorder to function …

Background Accurate modeling of electrostatic potential and corresponding energies
becomes increasingly important for understanding properties of biological macromolecules …

The ϕ, ψ backbone angle distribution of small homopolymeric model peptides is
investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study …

We investigated the effects of 17 widely used atomistic molecular mechanics force fields
(MMFFs) on the structures and kinetics of amyloid peptide assembly. To this end, we …

Alzheimer's disease is associated with the abnormal self-assembly of the amyloid-β (Aβ)
peptide into toxic β-rich aggregates. Experimental studies have shown that hydrophobic …

The aim of this work is to investigate the effects of molecular mechanics force fields on
amyloid peptide assembly. To this end, we performed extensive replica exchange molecular …

AMBER force fields are among the most commonly used in molecular dynamics (MD)
simulations of proteins. Unfortunately, they lack a specific set of lipid parameters, thus …

Recent experiments have shown that the congener Aβ1− 40 [D23− K28], in which the side
chains of charged residues Asp23 and Lys28 are linked by a lactam bridge, forms amyloid …

Small oligomers formed early along human islet amyloid polypeptide (hIAPP) aggregation is
responsible for the cell death in Type II diabetes. The epigallocatechin gallate (EGCG), a …