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A new definition and properties of the similarity value between two protein structures

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Abstract

Knowledge regarding the 3D structure of a protein provides useful information about the protein’s functional properties. Particularly, structural similarity between proteins can be used as a good predictor of functional similarity. One method that uses the 3D geometrical structure of proteins in order to compare them is the similarity value (SV). In this paper, we introduce a new definition of the SV measure for comparing two proteins. To this end, we consider the mass of the protein’s atoms and concentrate on the number of protein’s atoms to be compared. This defines a new measure, called the weighted similarity value (WSV), adding physical properties to geometrical properties. We also show that our results are in good agreement with the results obtained by TM-SCORE and DALILITE. WSV can be of use in protein classification and in drug discovery.

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Notes

  1. When the TM-SCORE is less than 0.2 it corresponds to randomly chosen unrelated proteins whereas with a score higher than 0.5 we generally assume the same fold in SCOP/CATH [21]. Here we normalized the TM-SCORE to 0.5 (i.e., we divided it by 2).

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Acknowledgments

I thank Dr. Jack A. Tuszynski (University of Alberta) for his helpful comments.

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  1. Department of Physics, Ferdowsi University of Mashhad, Mashhad, 9177948974, Iran

    S. M. Saberi Fathi

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  1. S. M. Saberi Fathi
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Saberi Fathi, S.M. A new definition and properties of the similarity value between two protein structures. J Biol Phys 42, 621–636 (2016). https://doi.org/10.1007/s10867-016-9429-0

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