Despite the recent advancements by deep learning methods such as AlphaFold2, in silico
protein structure prediction remains a challenging problem in biomedical research. With the …

Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional
conformations have been longstanding challenges in research on molecular recognition …

Methods that combine collective variable (CV) based enhanced sampling and global
tempering approaches are used in speeding‐up the conformational sampling and free …

Computer simulation methods can aid in the rational design of drugs aimed at a specific
target, typically a protein. The affinity of a drug for its target is given by the free energy of …

Polypeptoids are N-substituted glycine polymers, which differ from peptides in the placement
of the side chain on the amide nitrogen rather than the Cα carbon. A peptoid with a chiral …

The helicase protein of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-
2) is both a good potential drug target and very flexible. The flexibility, and therefore its …

Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both
cis and trans conformations. The transition between the two conformations requires …

A thermal responsive block copolymer made up of ethylene oxide (EO) and propylene oxide
(PO) blocks was simulated with optimized atomistic potentials and enhanced sampling …