In biomolecular systems (especially all-atom models) with many degrees of freedom such as
proteins and nucleic acids, there exist an astronomically large number of local-minimum …

We propose a new algorithm for obtaining proton titration curves of ionizable residues. The
algorithm is a pH replica‐exchange method (PHREM), which is based on the constant pH …

We propose a new method for molecular dynamics and Monte Carlo simulations, which is
referred to as the replica-permutation method (RPM), to realize more efficient sampling than …

We give general formulations of the multidimensional multicanonical algorithm, simulated
tempering, and replica-exchange method. We generalize the original potential energy …

We present a new type of the Hamiltonian replica-exchange method, where the van der
Waals radius parameter and not the temperature is exchanged. By decreasing the van der …

We investigated the transformation between the α-helix and β-hairpin structures of an 18-
residue design peptide, whose sequence is INYWLAHAKAGYIVHWTA. This peptide has …

Partial multicanonical algorithm is proposed for molecular dynamics and Monte Carlo
simulations. The partial multicanonical simulation samples a wide range of a part of the …

Amyloid-β peptides are known to form amyloid fibrils and are considered to play an
important role in Alzheimer's disease. Amyloid-β (29− 42) is a fragment of the amyloid-β …

We propose a new type of the Hamiltonian replica‐exchange method (REM) for molecular
dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM …

Computational protein structure prediction remains a challenging task in protein
bioinformatics. In the recent years, the importance of template‐based structure prediction is …