Molecular Dynamics Simulation

Cooperative “folding transition” in the sequence space facilitates function-driven evolution of protein families
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas …
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A new look at an old view of denaturant induced protein unfolding
We re-examine a site-binding approach independently proposed by Schellman (Schellman, J.A. (1958) Compt. rend. Lab. Carlsberg Ser. …
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New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of …
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Protein Data Bank Japan (PDBj): Updated user interfaces, resource description framework, analysis tools for large structures
The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (ww- PDB), accepts and processes the …
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Molmil: A molecular viewer for the PDB and beyond
We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has …
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Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins
Background: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) …
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Specific non-local interactions are not necessary for recovering native protein dynamics
The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need …
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Rigid-body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape-dependent manner
To understand the dynamic aspects of multispecificity of ubiquitin, we studied nine ubiquitin-ligand (partner protein) complexes by …
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Exhaustive comparison and classification of ligand-binding surfaces in proteins
Many proteins function by interacting with other small molecules (ligands). Identification of ligand-binding sites (LBS) in proteins …
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Counterbalance of ligand-and self-coupled motions characterizes multispecificity of Ubiquitin
Date hub proteins are a type of proteins that show multispecificity in a time-dependent manner. To understand dynamic aspects of such …
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