Abstract
Small world network concepts provide many new opportunities to investigate the complex three dimensional structures of protein molecules. This mini-review explores the published literature on using small-world network approaches to study protein structure, with emphasis on the different combinations of descriptors that have been tested, on studies involving ligand binding in protein-ligand complexes, and on protein-protein complexes. The benefits and success of small world network approaches, which change the focus from specific interactions to the local environment, even to non-local phenomenon, are described. The purpose is to show the different ways that small world network concepts have been used for building new computational models for studying protein structure and function, and for extending and improving existing modelling approaches.
Highlights
A fundamental tenet in the study of chemistry is the direct of just the binding site region; usually including hydrogen atoms relationship between structure, and chemical and physical properties. directed toward their hydrogen bonding partners
The role of specific water molecules, etc, provides a vast array of new what is interesting is that both rigidity and flexibility are information for understanding ligand binding [4]
Proteins are synthesised as linear polypeptides that view is often a less detailed schematic representation of 3D structure, fold into compact three dimensional conformations consisting of a highlighting the alpha helices, beta sheets, and loops
Summary
A fundamental tenet in the study of chemistry is the direct of just the binding site region; usually including hydrogen atoms relationship between structure, and chemical and physical properties. directed toward their hydrogen bonding partners. The role of specific water molecules, etc, provides a vast array of new what is interesting is that both rigidity and flexibility are information for understanding ligand binding [4]. Despite the large number of inter-residue close-contacts They bind with other lower detail, this level of analysis provides the best insight into overall folded proteins and/or small molecules, often adapting to the shape topology and stability. Comparing and contrasting and electrostatic requirements of these complexes It is the intrinsic schematic representations helps with the elucidation of function and complexity of the three dimensional conformations of proteins, and functional relationships; leads to powerful classification schemes; and the important role that proteins play in living organisms, that lead provides insights into evolutionary relationships [5].
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