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Special Issue

Progress of Theoretical and Computational Biophysics (Nov., 2019)

Preface of Special Issue

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

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