Progress of theoretical and computational biophysics—in honor of Professor Nobuhiro Go’s outstanding contribution on the occasion of his 80th birthday
Mikio Kataoka, Akio Kitao, Hidetoshi Kono
vol. 16, pp. 173-175
Released: November 29, 2019 |
Confirmation of the formation of salt bridges in the denatured state of CutA1 protein using molecular dynamics simulations
Katsuhide Yutani, Yoshinori Matsuura, Yasumasa Joti |
Energetics of cosolvent effect on peptide aggregation
Nobuyuki Matubayasi, Keiichi Masutani |
Replica exchange molecular dynamics simulation study on the mechanism of desiccation-induced structuralization of an intrinsically disordered peptide as a model of LEA proteins
Tatsushi Nishimoto, Yuta Takahashi, Shohei Miyama, Tadaomi Furuta, Minoru Sakurai |
Normal mode analysis calculation for a full-atom model with a smaller number of degrees of freedom for huge protein molecules
Shigeru Endo, Hiroshi Wako |
How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
Hiroshi Nakagawa, Mikio Kataoka |
Dynamic properties of oligomers that characterize low-frequency normal modes
Hiroshi Wako, Shigeru Endo |
Allosteric response to ligand binding: Molecular dynamics study of the N-terminal domains in IP3 receptor
Kei Moritsugu, Tsubasa Ito, Akinori Kidera |
Cancellation between auto- and mutual correlation contributions of protein/water dynamics in terahertz time-domain spectra
Yasumasa Joti, Akio Kitao |
Gō model revisited
Shoji Takada |
Snake cube puzzle and protein folding
Nobuhiro Go |
A collective motion description of tubulin βT7 loop dynamics
Sarbani Chattopadhyaya, Debamitra Chakravorty, Gautam Basu |
Mechanism of the light-driven proton pump of bacteriorhodopsin based on the consistency principle
Mikio Kataoka, Hironari Kamikubo |
All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins
Ryotaro Koike, Motonori Ota |
Prediction of the secondary structure of short DNA aptamers
Arina Afanasyeva, Chioko Nagao, Kenji Mizuguchi |
More efficient screening of protein-protein complex model structures for reducing the number of candidates
Kazuhiro Takemura, Akio Kitao |
Consistency principle for protein design
Rie Koga, Nobuyasu Koga |
Building a macro-mixing dual basin Gō model using the Multistate Bennett Acceptance Rati
Ai Shinobu, Chigusa Kobayashi, Yasuhiro Matsunaga, Yuji Sugita |
Normal mode analysis and beyond
Takahisa Yamato, Olivier Laprévote |
Methodological improvements for the analysis of domain movements in large biomolecular complexes
Ruth Veevers, Steven Hayward |
Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome
Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida |
Protein structure predictions by enhanced conformational sampling methods
Yuko Okamoto |
Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching
Miki Nakano, Osamu Miyashita, Florence Tama |
Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments
Toru Ekimoto, Yuichi Kokabu, Tomotaka Oroguchi, Mitsunori Ikeguchi |
Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot
Takeshi Kawabata |
Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory
Yutaka Maruyama, Hiroshi Takano, Ayori Mitsutake |
Characterization of X-ray diffraction intensity function from a biological molecule for single particle imaging
Atsushi Tokuhisa |
On the use of algebraic topology concepts to check the consistency of genome assembly
Jean-François Gibrat |
Mutational effects of Cys113 on structural dynamics of Pin1
Teikichi Ikura, Yasushige Yonezawa, Nobutoshi Ito |
Polymer brush in articular cartilage lubrication: Nanoscale modelling and simulation
Nobuhiko Kajinami, Mitsuhiro Matsumoto |
Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators
Bang-Chieh Huang, Lee-Wei Yang |
A tool written in Scala for preparation and analysis in MD simulation and 3D-RISM calculation of biomolecules
Itaru Onishi, Hiroto Tsuji, Masayuki Irisa |