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The paper describes the application of graph theoretic concepts to the dynamic cross-correlation data obtained from MD simulations of adenine riboswitch, in the absence and presence of adenine. This novel approach combines both community detection algorithms that support edge weights, and cliques. The effect of variations in the values of nearest neighbors (NN) and correlation coefficient threshold...
Interactions between large biomolecules and smaller bio-active ligands are usually studied through a process called docking. Its aim is to find an energetically favorable orientation of a ligand within an active site of a biomolecule. Chemical reactions take place in active site and the role of the ligand is either to speed up, slow down or change the reaction (e.g., an enzyme catalyzed hydrolysis),...
Biomolecules, especially proteins, often consist of several rigid subunits and work like mechanical devices. Therefore their mechanical motion or the conformational dynamics are significantly investigated with a great deal of interests. However, it is a challenge to detect small mechanical motion, especially when its dimension is as small as several nanometers. Single molecule measurement technique...
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