Related papers: A classification scheme of Amino Acids in the Gene…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
Continuing our attempt to explain the degeneracy of the genetic code using basic classical Lie superalgebras, we present the branching schemes for the typical codon representations (typical 64-dimensional irreducible representations) of…
We develop a simple optimization procedure for assigning binary values to the amino acids. The binary values are determined by a maximization of the degree of pattern conservation in groups of closely related protein sequences. The…
In this work it is shown that three pairs of the factors appear to be the key, i.e. main factors of a natural classification of protein (canonical) amino acids within the amino acid (genetic) code. First pair: the factors of the habit of an…
A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is…
Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…
The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the Mean Square measure as a function quantifying error robustness, a value can be obtained for a genetic…
Group theoretical concepts are invoked in a specific model to explain how only twenty amino acids occur in nature out of a possible sixty four. The methods we use enable us to justify the occurrence of the recently discovered twenty first…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the…
This paper reports about an approach to the classification of proteins' primary structures taking advantage of the Self Organizing Maps algorithm and of a numerical coding of the aminoacids based upon their physico-chemical properties.…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
The quantum enveloping algebra U_q(sl(2) \oplus sl(2)) in the limit q \to 0 is proposed as a symmetry algebra for the genetic code. In this approach the triplets of nucleotids or codons in the DNA chain are classified in crystal bases,…
A pattern Recognition of a probability distribution of amino acids is obtained for selected families of proteins. The mathematical model is derived from a theory of protein families formation which is derived from application of a Pauli's…
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 "golden" amino acids, 7 of their…
In the present work, 16 genetic code doublets and their cognate amino acids in the genetic code are fitted into a polyhedron model. Based on the structural regularity in nucleobases, and by using a series of common-sense topological…
Upon the covalent-bonding hybrid of the nitrogen atoms taken as a measure for the structural regularity in nucleobases, it can be identified that the internal relation within the 20 amino acids follows a cooperative vector-in-space addition…
We introduce the simple parametrization for the space of codons (triples of nucleotides) by 8\times 8 table. This table (which we call the dyadic plane) possesses the natural 2-adic ultrametric. We show that after this parametrization the…
In this paper it is shown that within a Combined Genetic Code Table, realized through a combination of Watson-Crick Table and Codon Path Cube it exists, without an exception, a strict distinction between two classes of enzymes…