3D structural analysis of proteins using electrostatic surfaces based on image segmentation

Dimitrios Vlachakis; Spyridon Champeris Tsaniras; Georgia Tsiliki; Vasileios Megalooikonomou; Sophia Kossida

3D structural analysis of proteins using electrostatic surfaces based on image segmentation

Dimitrios Vlachakis, Spyridon Champeris Tsaniras, Georgia Tsiliki, Vasileios Megalooikonomou, Sophia Kossida

Abstract

Herein, we present a novel strategy to analyse and characterize proteins using protein molecular electrostatic surfaces. Our approach starts by calculating a series of distinct molecular surfaces for each protein that are subsequently flattened out, thus reducing 3D information noise. RGB images are appropriately scaled by means of standard image processing techniques whilst retaining the weight information of each protein’s molecular electrostatic surface. Then homogeneous areas in the protein surface are estimated based on unsupervised clustering of the 3D images, while performing similarity searches. This is a computationally fast approach, which efficiently highlights interesting structural areas among a group of proteins. Multiple protein electrostatic surfaces can be combined together and in conjunction with their processed images, they can provide the starting material for protein structural similarity and molecular docking experiments.

Keywords

protein function; molecular docking; three-dimensional structure; image segmentation; molecular surface; similarity searches

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