Molecular Dynamics Simulation

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures
Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions …
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Composite structural motifs of binding sites for delineating biological functions of proteins
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn …
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GIRAF: A method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution
Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational …
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Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes …
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