Many proteins contain disulfide bonds that are usually essential for maintaining function and
a stable structure. Several algorithms attempt to predict the arrangement of disulfide bonds …

Three algorithms, namely, a replica exchange method (REM), a replica exchange
multicanonical method (REMUCA), and a replica exchange multicanonical method with …

We describe the application of our recently proposed method of hierarchical optimization of
the protein energy landscape to optimize our off-lattice united-residue (UNRES) force field …

A key regulator of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor
traffic, PICK1 is known to interact with over 40 other proteins, including receptors …

Molecular dynamics (MD) simulations generate a canonical ensemble only when integration
of the equations of motion is coupled to a thermostat. Three extended phase space …

The implementation of molecular dynamics with the united-residue (UNRES) force field is
extended to treat multichain proteins. Constant temperature was maintained in the …

We introduce a nonradial potential term for coarse-grained (CG) molecular simulations of
proteins. This term mimics the backbone dipole− dipole interactions and accounts for the …

We report the application of the hierarchical optimization method of protein potential-energy
landscapes described in the accompanying papers (Liwo, A.; Arłukowicz, P.; Ołdziej, S.; …

Coarse-grained models are useful tools to investigate the structural and thermodynamic
properties of biomolecules. They are obtained by merging several atoms into one interaction …

We report the implementation of our united-residue UNRES force field for simulations of
protein structure and dynamics with massively parallel architectures. In addition to coarse …