We provide an overview of the IMPACT molecular mechanics program with an emphasis on
recent developments and a description of its current functionality. With respect to core …

The construction of complex protein folds relies on the precise conversion of a linear
polypeptide chain into a compact 3-dimensional structure. The interplay of forces that link …

The primary sequence of a biopolymer encodes the essential information for folding,
permitting to carry out sophisticated functions. Inspired by natural biopolymers, peptide and …

While the quality of the current CHARMM22/CMAP additive force field for proteins has been
demonstrated in a large number of applications, limitations in the model with respect to the …

Some frequently encountered deficiencies in all-atom molecular simulations, such as
nonspecific protein–protein interactions being too strong, and unfolded or disordered states …

The generalized Born (GB) model is one of the fastest implicit solvent models, and it has
become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with …

Background Nonadditivity in fitness effects from two or more mutations, termed epistasis, can
result in compensation of deleterious mutations or negation of beneficial mutations. Recent …

Presented is a polarizable force field based on a classical Drude oscillator framework,
currently implemented in the programs CHARMM and NAMD, for modeling and molecular …

The transcription factor NF-E2-related factor 2 (Nrf2) is a master regulator of a genetic
program, termed the phase 2 response, that controls redox homeostasis and participates in …

A structural motif, the tryptophan zipper (trpzip), greatly stabilizes the β-hairpin conformation
in short peptides. Peptides (12 or 16 aa in length) with four different turn sequences are …