shiyi shen

Analysis of Protein Three-Dimension Structure Using Amino Acids Depths

Protein Journal, 2007

The issue of amino acid depth in proteins gives important insights to our understanding of protei... more The issue of amino acid depth in proteins gives important insights to our understanding of protein’s three-dimensional structure. There has already been much research done in mathematical and statistical sciences regarding the general definitions, properties and algorithms describing the particle depth of spatially extended systems. We constructed a method of calculating the amino acids depths and applied it to a set of 527 protein structures. We propose the introduction of amino acid depth tendency factors for three-dimensional structures of proteins. The depth tendency factors relate not only to the hydrophobicity indices but also to the electrostatic charge. We found a relationship between the protein size and the number of residues using the distance between the deepest residue and surface residues. We made a prediction regarding the number of residues on the surface of a protein, the deepest amino acid, and the average depth, all of which are fitted well to a linear functional relationship with the length of the protein. Finally, we have predicted the depths of multiple peptides in protein’s three-dimension structure.

format_quoteA comprehensive Depth Database of 527 protein structures enables calculation of amino acid depths and their distribution in protein space.format_quote

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On the evolution rate in mammalian mitochondrial genomes

Computational Biology and Chemistry / Computers & Chemistry, 2011

The methods of phylogenetic inference have become more and more realistic and effective since the... more The methods of phylogenetic inference have become more and more realistic and effective since the evolution rate was taken into account. In order to study the evolution rate more comprehensively, all 13 protein coding genes in 123 mammalian mitochondrial genomes are analyzed. The evolution rates of different codon position are analyzed as well. The evolution rate is estimated by Shannon entropy. We find that the distribution of 3rd codon position doesn't follow gamma distribution and the results suggest that it follows a mixed distribution of gamma distribution and normal distribution. The relationship between different codon positions is also studied. We find that there are significant positive correlation between three codon positions. Especially between 1st codon position and 2nd codon position, there is strong linear relationship.

format_quoteAnalysis reveals that evolution rates at the 3rd codon position do not fit a gamma distribution, indicating unique evolutionary dynamics.format_quote

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SMA: An Efficient Tool for Large-Scale Multiple Alignment

To compare large numbers of genomic sequences of related virus, such as HIV and SARS, biologists ... more

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On the expectation and variance of hamming distance between two i.i.d random vectors

Acta Mathematicae Applicatae Sinica-english Series, 1997

By using the generalized MacWilliams theorem, we give new representations for expectation and var... more

On the mean value and variance of distance distribution of non-linear codes in GF( q

Journal of Electronics (china), 1998

This paper presents the lower bounds and upper bounds for the mean value and variance of distance... more

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