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Conformational change of proteins arising from normal mode calculations.
A normal mode analysis of 20 proteins in 'open' or 'closed' forms was performed using simple potential and protein models. The quality of the results was found to depend upon the form of the protein… Expand
Building-block approach for determining low-frequency normal modes of macromolecules.
Normal mode analysis of proteins of various sizes, ranging from 46 (crambin) up to 858 residues (dimeric citrate synthase) were performed, by using standard approaches, as well as a recently proposed… Expand
Unveiling Molecular Mechanisms of Biological Functions in Large Macromolecular Assemblies Using Elastic Network Normal Mode Analysis
Molecular dynamics simulation shows large volume fluctuations of proteins
Abstract In this paper we present a new approach to study the volume fluctuations of proteins. From a 1 ns molecular dynamics simulation, the volume fluctuation of human lysozyme has been calculated.… Expand
Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory
Abstract Thermodynamic properties of water molecules around single- and double-stranded DNAs (ssDNAs and dsDNAs) with different sequences were investigated using grid inhomogeneous solvation theory.… Expand
Normal Mode Analysis Techniques in Structural Biology
The dynamic simulation of macromolecular systems with biologically relevant sizes and time scales is critical for understanding macromolecular function. In this context, normal mode analysis (NMA)… Expand
Coarse-Grained Normal Mode Analysis to Explore Large-Scale Dynamics of Biological Molecules
共溶質存在下におけるDNA水和水の熱力学的性質の解析 | 文献情報 | J-GLOBAL 科学技術総合リンクセンター
Exploring Global Motions and Electrostatic Properties of the Ribosome
Shape equations for phospholipid vesicles including a spherical actin cortex are derived in 2 and 3 spatial dimensions. They arise from the condition of stationarity of the membrane free energy at… Expand