Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in
biology and human diseases. It is now also recognized that many IDPs remain dynamic …

We test a range of standard generalized Born (GB) models and protein force fields for a set
of five experimentally characterized, designed peptides comprising alternating blocks of …

A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain
number of explicit water molecules (Nwat) during the calculations, has been tested on a set …

Molecular dynamics (MD) simulation implemented with a state-of-the-art protein force field
and implicit solvent model is an attractive approach to investigate protein folding, one of the …

Alzheimer's disease is a neurodegenerative disorder linked to oligomerization and
fibrillization of amyloid β peptides, with Aβ1–42 being the most aggregative and neurotoxic …

2, 5-Dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 is a
mononuclear non-heme iron oxygenase responsible for the biodegradation of 2, 5 …

Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are
occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving …

Accelerated molecular dynamics (aMD) protocols were assessed on predicting the
secondary structure of eight peptides, of which two are helical, three are β-hairpins, and …

(-)-Spirobrassinin, a glucosinolate compound from Brassicaceae plants, has shown
inhibitory effects on weeds. However, its specific target sites are not well explored. This …