An Application of the Eigenproblem for Biochemical Similarity

Symmetry

Dan-Marian Joiţa¹  Donatella Bàlint¹  Lorentz Jäntschi¹  Mihaela Aurelia Tomescu² 

[1] Chemistry Doctoral School, Babeş-Bolyai University, 400084 Cluj, Romania;Department of Mathematics and Informatics, University of Petroșani, 332006 Hunedoara, Romania;

关键词: eigenproblem;    eigenvalues;    molecular alignment;    orthogonal alignment;    biochemical similarity;    antisymmetric matrix;   

DOI  :  10.3390/sym13101849

来源: DOAJ

【 摘 要 】

Protein alignment finds its application in refining results of sequence alignment and understanding protein function. A previous study aligned single molecules, making use of the minimization of sums of the squares of eigenvalues, obtained for the antisymmetric Cartesian coordinate distance matrices D_x and D_y. This is used in our program to search for similarities between amino acids by comparing the sums of the squares of eigenvalues associated with the D_x, D_y, and D_z distance matrices. These matrices are obtained by removing atoms that could lead to low similarity. Candidates are aligned, and trilateration is used to attach all previously striped atoms. A TM-score is the scoring function that chooses the best alignment from supplied candidates. Twenty essential amino acids that take many forms in nature are selected for comparison. The correct alignment is taken into account most of the time by the alignment algorithm. It was numerically detected by the TM-score 70% of the time, on average, and 15% more cases with close scores can be easily distinguished by human observation.

【 授权许可】

Unknown