Tensor Algebra-based Geometrical (3D) Biomacro-Molecular Descriptors for Protein Research: Theory, Applications and Comparison with other Methods

Scientific Reports
Julio E TeránF Javier Torres

Abstract

In this report, a new type of tridimensional (3D) biomacro-molecular descriptors for proteins are proposed. These descriptors make use of multi-linear algebra concepts based on the application of 3-linear forms (i.e., Canonical Trilinear (Tr), Trilinear Cubic (TrC), Trilinear-Quadratic-Bilinear (TrQB) and so on) as a specific case of the N-linear algebraic forms. The definition of the kth 3-tuple similarity-dissimilarity spatial matrices (Tensor's Form) are used for the transformation and for the representation of the existing chemical information available in the relationships between three amino acids of a protein. Several metrics (Minkowski-type, wave-edge, etc) and multi-metrics (Triangle area, Bond-angle, etc) are proposed for the interaction information extraction, as well as probabilistic transformations (e.g., simple stochastic and mutual probability) to achieve matrix normalization. A generalized procedure considering amino acid level-based indices that can be fused together by using aggregator operators for descriptors calculations is proposed. The obtained results demonstrated that the new proposed 3D biomacro-molecular indices perform better than other approaches in the SCOP-based discrimination and the prediction o...Continue Reading

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Citations

Dec 28, 2019·Biomolecules·Guillermin Agüero-ChapinAgostinho Antunes
Jun 4, 2021·Journal of Chemical Information and Modeling·Sergio A Pinacho-CastellanosCarlos A Brizuela
Oct 31, 2019·Journal of Chemical Information and Modeling·Ernesto Contreras-TorresJuan Carlos Sánchez-Rodríguez

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Methods Mentioned

BETA
protein folding

Software Mentioned

MCoMPAs
QuBiLs MIDAS
TOpological MOlecular Modelling Science
MOBYDIGS
- CAMPS
MuLiMs
WEKA
QuBiLs MAS (
ToMoCoMD
BLAST

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