Internet Electronic Journal of Molecular Design

Based on the structure information of the mathematical characteristics of the degree distribution of saturated hydrocarbons, a method to count the branching number of a saturated hydrocarbon is proposed and then extended to general molecules. In order to understand the structure information of the characteristics, some new concepts are introduced, and the edges in a molecule are partitioned into different cases. In the understanding, the edges that are essential to connecting the cycles are not considered as the branches. Subsequently, several formulas are tried to calculate the proposed branching number. Then, the formulas are generalized to other molecules with poly–cycles, heteroatoms and/or multiple bonds. Most of molecules are counted in agreement with intuitive view, but there also exits some molecules that are difficult to judge the branching numbers. Th

The Topological Index Z Before and After 1971

The author’s first paper on the topological index Z was published in Bull. Chem. Soc. Jpn. in 1971, where good correlation was found between the boiling points of alkane isomers and their Z values. This idea is based on the author’s unpublished work performed in 1957, when the boiling points of octane isomers were predicted by scrutinizing the structural dependency of boiling points of alkanes up to heptane. Behind stories inside and outside of the country before and after the birth of Z index are introduced. Several academic encounters of the author and reactions of the contemporary chemists to the new idea are also described. In the end some aspects of QSAR problems for octane isomers are introduced

The Numerical Characterization and Similarity Analysis of DNA Primary Sequences #

Motivation. DNA sequencing has become routine and has resulted in an abundance of data on primary sequences of DNA for various species. Hence, we faced the task of process such great amount of data, which poses a number of yet unsolved problems. The motivation of this paper is to introduce a new numerical characterization of DNA sequences. Method. We define a scheme to give a logic order of DNA primary sequences in term of the classification of nucleic acid bases. Using logic sequences we generate a set of 4×6 matrices to represent DNA primary sequences, which are based on counting all (0,1) triplets in the logic sequences. Using the condensed representation of primary DNA primary sequences and the eigenvalues of the corresponding symmetric real matrix a comparison is made between the primary sequences for exon–1 of human �–globin and seven other species. Results. With this procedure we extend the matrix method to determine new invariants as descriptors for DNA sequences

Investigations on Evolutionary Changes in Base Distributions

Motivation. We had observed that 2D graphical plots of DNA sequences show apparently systematic variations among members of families of gene sequences and reported these to be due to evolutionary changes. Investigations of phylogenetic relationships between species through studies of gene sequences has been one of the prime areas of interest to molecular biologists. While questions such as rate of mutational changes in DNA sequences have been investigated extensively, attention is being given recently to changes in base distribution within such sequences. Roman–Roldan et al has shown that complexity of base organization in intron segments increases with evolution. Method. We use the 2D graphical representation method to map the DNA sequences and use four numerical techniques to quantitatively measure the differences observed in the different gene sequences. Results. We report here our investigations using a graphical technique for DNA sequence representation and related analyses for conserved gene sequences such as kinetoplasts, heat shock proteins, globins and others

Numerical characterization of DNA primary sequence, Internet

Special issue dedicated to Professor Haruo Hosoya on the occasion of the 65 th birthda

Finding Protein Coding Genes in the Yeast Genome Based on the Characteristic Sequences #

Motivation. Due to the rapid growth of DNA sequences data in various databases, the development of accurate algorithms for gene prediction is of great importance. The motivation of this paper is to suggest a numerical characterization algorithm specific for predicting protein–coding genes in the yeast genome. Method. The characteristic sequences of a DNA sequence are a group of (0,1) sequences. Each of them is a reduced representation of the given DNA sequence, and two of them can uniquely reconstruct the sequence. Based on the numerical description of the characteristic sequences, a protein coding gene finding algorithm specific for the yeast genome was suggested

Internet Electronic Journal of Molecular Design

BioChem Pres

Internet Electronic Journal of Molecular Design

Inhibition by 2,3�Diarylcyclopentenones Based on MEDV–13, Internet Electron. J. Mol. Des

A Modified Distance Matrix to Distinguish Cis/Trans Isomers

The general distance matrix D was modified to distinguish cis/trans isomers of cycloalkanes. A new topological index, VDI(±1), was derived from the modified distance matrix (Dmod) according to the calculation of VDI proposed in a previous paper. This new structural descriptor discriminates all compounds studied in this paper. The regression analysis against the boiling temperatures (tb) for 53 cis/trans isomers of cycloalkanes with VDI(±1) and other topological indices gives a high correlation coefficient (r = 0.9961) and low standard deviation (s = 3.31 ºC), which is much better than that obtained with VDI(0). Keywords. Topological index; boiling temperature; quantitative structure–property relationships; QSPR; molecular graph; structural descriptor; distance matrix.