Skeleton-based shape analysis of protein models

•We propose a new protein shape analysis method based on the protein skeleton.•We extract the skeleton based on the improved MRG method, which can describe the correct topology and detail of protein models.•The local diameter method based on our improved skeleton extraction is as good as standard methods and sometimes achieves better shape analysis results of protein models.•Our shape analysis method is also applicable for the models with large deformations.

In order to compare the similarity between two protein models, a shape analysis algorithm based on skeleton extraction is presented in this paper. It firstly extracts the skeleton of a given protein surface by an improved Multi-resolution Reeb Graph (MRG) method. A number of points on the model surface are then collected to compute the local diameter (LD) according to the skeleton. Finally the LD frequency is calculated to build up the line chart, which is employed to analyze the shape similarity between protein models. Experimental results show that the similarity comparison using the proposed shape descriptor is more accurate especially for protein models with large deformations.

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