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Статья

Deciphering Fine Molecular Details of Proteins’ Structure and Function with a Protein Surface Topography (PST) Method

Journal of Chemical Information and Modeling. 2014. Vol. 54. No. 4. P. 1189-1199.
Efremov R., Koromyslova A. D., Chugunov A. O.

Molecular surfaces are one of the key players in processes of bimolecular recognition and interaction. Nowadays, state of the art methods exist for visualizing molecule surface and surface distributed properties in three-dimensional space. However, such visual information could only be analyzed by human eye and therefore prompt to be biased and onerous in case of large sets of objects. Here we present a method to create 2D projections or ”earth maps” of whole protein surface – protein surface topography (PST). Representing complex molecule surfaces as an array of data gives the advantage of simple and pictorial visualization of surface properties. PST can be used to easy visualize conformational changes between different states of molecules, perform group analysis, and reveal common patterns or dissimilarities. It is useful tool to add to docking experiments, illustrating complementary features between ligand and receptor surfaces.