Search Results - "Gō, Nobuhiro"

Ligand-Induced Protein Responses and Mechanical Signal Propagation Described by Linear Response Theories by Yang, Lee-Wei, Kitao, Akio, Huang, Bang-Chieh, Gō, Nobuhiro

“…In this study, a general linear response theory (LRT) is formulated to describe time-dependent and -independent protein conformational changes upon CO binding…”
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Snake cube puzzle and protein folding by Go, Nobuhiro

“…The snake cube puzzle made of a linear array of 27 cubes and its modified and extended versions are used as theoretical models to study the mechanism of…”
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Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites by Kawabata, Takeshi, Go, Nobuhiro

“…One of the simplest ways to predict ligand binding sites is to identify pocket‐shaped regions on the protein surface. Many programs have already been proposed…”
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Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis by Hayward, S, Kitao, A, Go, N

“…A comparison of a normal mode analysis and principal component analysis of a 200-ps molecular dynamics trajectory of bovine pancreatic trypsin inhibitor in…”
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Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data by Kidera, A, Go, N

“…A dynamic structure refinement method for X-ray crystallography, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in…”
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Effect of solvent on collective motions in globular protein by Hayward, S, Kitao, A, Hirata, F, Go, N

“…Two molecular dynamics simulations on bovine pancreatic trypsin inhibitor (BPTI), have been made, one in vacuum, the other in water, in order to assess the…”
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Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis by Hayward, Steven, Kitao, Akio, Gō, Nobuhiro

“…A comparison is made between a 200‐ps molecular dynamics simulation in vacuum and a normal mode analysis on the protein bovine pancreatic trypsin inhibitor…”
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Common spatial arrangements of backbone fragments in homologous and non-homologous proteins by Alexandrov, N N, Takahashi, K, Go, N

“…We have developed a new method of detecting common spatial arrangements of backbone fragments in proteins. This method allows corresponding fragments to occur…”
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Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction by Kim, Oanh T.P, Yura, Kei, Go, Nobuhiro

“…Protein-RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and…”
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Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme by Horiuchi, T, Go, N

“…A method is presented to describe the internal motions of proteins obtained from molecular dynamics or Monte Carlo simulations as motions of normal mode…”
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Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins by Alexandrov, Nickolai N., Gō, Nobuhiro

“…We have completed an exhaustive search for the common spatial arrangements of backbone fragments (SARFs) in nonhomologous proteins. This type of local…”
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Normal mode refinement: crystallographic refinement of protein dynamic structure. II. Application to human lysozyme by Kidera, A, Inaka, K, Matsushima, M, Go, N

“…The dynamic structure of a protein, human lysozyme, is determined by the normal mode refinement of X-ray crystal structure. This method uses the normal modes…”
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A theorem on amplitudes of thermal atomic fluctuations in large molecules assuming specific conformations calculated by normal mode analysis by Go, N

“…An exact theorem is proved and its implication is discussed. The theorem states that, if a large molecule, typically biological macromolecules such as…”
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Energy landscape of a native protein: Jumping-among-minima model by Kitao, Akio, Hayward, Steven, Go, Nobuhiro

“…We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping‐among‐minima (JAM)…”
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Conformational deformation in deoxymyoglobin by hydrostatic pressure by Yamato, T, Higo, J, Seno, Y, Go, N

“…Pressure effect on the equilibrium conformation in sperm whale deoxymyoglobin and its volume fluctuation are studied by the normal mode analysis and strain…”
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Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property by Nishikawa, T, Go, N

“…The normal mode analysis of conformational fluctuation is carried out for a small globular protein, bovine pancreatic trypsin inhibitor. Results are analyzed…”
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FEDER/2: program for static and dynamic conformational energy analysis of macro-molecules in dihedral angle space by Wako, Hiroshi, Endo, Shigeru, Nagayama, Kuniaki, Gō, Nobuhiro

“…The computer program, FEDER/2, has been developed to carry out static and dynamic conformational energy analysis of macromolecules by treating dihedral angles…”
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BAAQ: An Infrastructure for Application Integration and Knowledge Discovery in Bioinformatics by Xiujun Gong, Nakamura, K., Hua Yu, Kei Yura, Nobuhiro Go

“…The emerging grid computing technologies enable bioinformatics scientists to conduct their researches in a virtual laboratory, in which they share public…”
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Switch Interactions Control Energy Frustration and Multiple Flagellar Filament Structures by Kitao, Akio, Yonekura, Koji, Maki-Yonekura, Saori, Samatey, Fadel A., Imada, Katsumi, Namba, Keiichi, Go, Nobuhiro

“…Bacterial flagellar filament is a macromolecular assembly consisting of a single protein, flagellin. Bacterial swimming is controlled by the conformational…”
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Structural basis of hierarchical multiple substates of a protein. I: Introduction by Noguti, T, Go, N

“…A computer experiment of protein dynamics is carried out, which consists of two steps: (1) A Monte Carlo simulation of thermal fluctuations in the native state…”
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