Molecular Mechanics (MM) force fields are the methods of choice for protein simulations,
which are essential in the study of conformational flexibility. Given the importance of protein …

In this perspective, we review the theory and methodology of the derivation of force fields
(FFs), and their validity, for molecular simulations, from their inception in the second half of …

The theory of intermolecular forces has advanced very greatly in recent years. It has become
possible to carry out accurate calculations of intermolecular forces for molecules of useful …

An accurate scoring function is a key component for successful protein structure prediction.
To address this important unsolved problem, we develop a generalized orientation and …

The first systematic overviews on global optimization appeared in 1975–1978 thanks to two
fundamental volumes titled Towards Global Optimization (Dixon & Szegö, 1975, 1978). At …

GROMOS++ is a set of C++ programs for pre-and postprocessing of molecular dynamics
simulation trajectories and as such is part of the GRO ningen MO lecular S imulation …

Background: Design of small molecules which are able to bind to the protein responsible for
a disease is the key step of the entire process of the new medicine discovery. Atomistic …

Diabetes mellitus is a serious metabolic disorder characterized by abnormal blood glucose
levels in the body. The development of therapeutic strategies for restoring and maintaining …

Recently, we developed a residue-specific force field (RSFF1) based on conformational free-
energy distributions of the 20 amino acid residues from a protein coil library. Most …

Molecular simulations are an excellent tool to study adsorption and diffusion in nanoporous
materials. Examples of nanoporous materials are zeolites, carbon nanotubes, clays, metal …