Browsing Division of Bioinformatics (DIC) by Title
Now showing items 1-20 of 83
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3(10)-Helix Adjoining a -Helix and b -Strand: Sequence and Structural Features and Their Conservation
(WILEY-BLACKWELL, 2005-06-15)Does the amino acid use at the terminal positions of an a-helix become altered depending on the context-more specifically. when there is an adjoining 3(10)-helix, and can a single helical cylinder encompass the resultant ... -
Compositional correlations in canine genome reflects similarity with human genes
(SPRINGER, 2006-05-31)The base compositional correlations that hold among various coding and noncoding regions of the canine genome have been analysed. The distribution pattern of genes, on the basis of GC 3 composition, shows a wide range ... -
The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes
(ELSEVIER SCIENCE, 2005-01-17)Fluctuations and increments of both C-3 and G(3) levels along the human coding sequences were investigated comparing two sets of Xenopus/human orthologous genes. The first set of genes shows minor differences of the GC(3) ... -
Compositional transitions between Oryza sativa and Arabidopsis thaliana genes are linked to the functional change of encoded proteins
(ELSEVIER SCIENCE, 2006-02)Compositional transition was previously reported between homologous pairs of Oryza sativa and Arabidopsis thaliana. We analysed 2041 homologous gene pairs of O. sativa and A. thaliana and found that the genes that underwent ... -
Conservation and relative importance of residues across protein-protein interfaces
(NATL ACAD SCIENCES, 2005-10-25)A core region surrounded by a rim characterizes biological interfaces. We ascertain the importance of the core by showing the sequence entropies of the residues comprising the core to be smaller than those in the rim. Such ... -
Conserved residue clusters at protein-protein interfaces and their use in binding site identification
(BIOMED CENTRAL, 2010-05-27)Background: Biological evolution conserves protein residues that are important for structure and function. Both protein stability and function often require a certain degree of structural co-operativity between spatially ... -
Correlations between genomic GC levels and optimal growth temperatures: some comments
(ACADEMIC PRESS, 2005-02-25)Regarding the existence of any specific correlation between optimal growth temperature and genomic GC levels, Musto et al. [FEBS Lett. 573 (2004) 73] have recently performed analysis on 20 prokaryotic families and showed ... -
Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of Escherichia coli genome
(ADENINE, 2008-06)Biased usage of synonymous codons has been elucidated under the perspective of cellular tRNA abundance and more recently by the mRNA secondary structure folding stability of the corresponding genes. Taking advantage of ... -
Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development
(SPRINGER, 2008-06)Cancer cells and tissues exhibit genome wide hypomethylation and regional hypermethylation. CpG-methylation of DNA ((Me)CpG-DNA) is defined as the formation of a C-C covalent bond between the 5'-C of cytosine and the -CH(3) ... -
Different functional classes of genes are characterized by different compositional properties
(ELSEVIER, 2007-12-22)A compositional analysis on a set of human genes classified in several functional classes was performed. We found out that the GC3, i.e. the GC level at the third codon positions, of the genes involved in cellular metabolism ... -
Differential Selective Constraints Shaping Codon Usage Pattern of Housekeeping and Tissue-specific Homologous Genes of Rice and Arabidopsis
(OXFORD UNIV, 2008-12)Intra-genomic variation between housekeeping and tissue-specific genes has always been a study of interest in higher eukaryotes. To-date, however, no such investigation has been done in plants. Availability of whole genome ... -
Domain analysis of a groundnut calcium-dependent protein kinase - Nuclear localization sequence in the junction domain is coupled with nonconsensus calcium binding domains
(AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY, 2006-04-14)The signature of calcium-dependent protein kinases (CDPKs) is a C-terminal calmodulin-like domain (CaMLD) with four consensus calcium-binding sites. A junction domain (JD) joins the kinase with CaMLD and interacts with ... -
Evolutionary constraints on hub and non-hub proteins in human protein interaction network: Insight from protein connectivity and intrinsic disorder
(ELSEVIER SCIENCE, 2009-04-01)It has been claimed that proteins with more interacting partners (hubs) are structurally more disordered and have a slow evolutionary rate. Here, in this paper we analyzed the evolutionary rate and structural disorderness ... -
Evolutionary forces in shaping the codon and amino acid usages in Bochmannia floridanus
(ADENINE PRESS,, 2004-08)Endosymbiotic relationship has great effect on ecological system. Codon and amino acid usages bias of endosymbiotic bacteria Blochmannia floridanus (whose host is an ant Camponotus floridanus) was investigated using ... -
Exploring the differences in evolutionary rates between monogenic and polygenic disease genes in human.
(Oxford University Press, 2010-04)Comparative analyses on disease and nondisease (ND) genes have greatly facilitated the understanding of human diseases. However, most studies have grouped all the disease genes together and have performed comparative ... -
Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network
(ELSEVIER, 2009-01-15)Evolutionary rates of party hub and date hub proteins of Saccharomyces cerevisiae are analyzed under the perspective of ordered/disordered ness of proteins and the three dimensional structural context such as the solvent ... -
Faculty Publication List : Dept. of Bioinformatics , 2000-01
(Bose Institute, 2001) -
Faculty Publication List : Dept. of Bioinformatics , 2001-02
(Bose Institute, 2002) -
Faculty Publication List : Dept. of Bioinformatics , 2002-03
(Bose Institute, 2003) -
Faculty Publication List : Dept. of Bioinformatics , 2003-04
(Bose Institute, 2004)