Haruki Nakamura

Announcing the worldwide Protein Data Bank

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

Protein Data Bank: the single global archive for 3D macromolecular structure data

The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has...

Conformational transition states of a β‐hairpin peptide between the ordered and disordered conformations in explicit water

Abstract The conformational transition states of a β‐hairpin peptide in explicit water were identified from the free energy landscapes obtained from the multicanonical ensemble,...

Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95

The C96 and AMBER95 force fields were compared with small model peptides Ac-(Ala)n-NMe (Ac = CH3CO, NMe = NHCH3, n=2 and 3) in vacuo and in TIP3P water by computing the free-ene...

Energy landscape of a peptide consisting of α‐helix, 3₁₀‐helix, β‐turn, β‐hairpin, and other disordered conformations

Abstract The energy landscape of a peptide [Ace‐Lys‐Gln‐Cys‐Arg‐Glu‐Arg‐Ala‐Nme] in explicit water was studied with a multicanonical molecular dynamics simulation, and the AMBER...