Division of Bioinformatics (DIC): Recent submissions
Now showing items 21-40 of 83
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ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces
(BIOMED CENTRA, 2006-06-07)Molecular recognition is all pervasive in biology. Protein molecules are involved in enzyme regulation, immune response, signal transduction, oligomer assembly, etc. Delineation of physical and chemical features of the ... -
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 ... -
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 ... -
Synonymous codon usage analysis of the mycobacteriophage Bxz1 and its plating bacteria M-smegmatis: Identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species
(SPRINGER SINGAPORE PTE LTD, 2004-07-31)The extent of codon usage in the protein coding genes of the mycobacteriophage, Bxz1, and its plating bacteria, M. smegmatis, were determined, and it was observed that the codons ending with either G and / or C were ... -
Structural identification of a novel thioredoxin SoxS: Prediction of the function in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle
(ELSEVIER SCIENCE, 2006-01-31)Microbial redox reactions involving inorganic Sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically ... -
Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle
(ELSEVIER SCIENCE, 2006-01-01)Microbial redox reactions involving inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically ... -
A structural study towards the understanding of the interactions of SoxY, SoxZ, and SoxB, leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon
(ACADEMIC PRESS, 2005-09-23)Microbial redox reactions of inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are mediated by phylogenetically diverse ... -
Role of mutational bias and natural selection on genome-wide nucleotide bias in prokaryotic organisms
(ELSEVIER SCI, 2005-07)Correlations between genomic GC contents and amino acid frequencies were studied in the homologous sequences of 12 eubacterial genomes. Results show that amino acids encoded by GC-rich codons increases significantly with ... -
On the origin of genomic adaptation at high temperature for prokaryotic organisms
(ELSEVIER SCIENCE, 2005-05-13)For a long time, the central issue of evolutionary genomics was to find out the adaptive strategy of nucleic acid molecules of various microorganisms having different optimal growth temperatures (T-opt). Long-standing ... -
Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene"
(ELSEVIER SCIENCE, 2005-05-20)Recently Anders Fuglsang provided a modified way for calculating N-c when biased discrepancy is present in a gene [Biochem. Biophys. Res. Commun. 317 (2004) 957]. Instead of taking the average codon homozygosity for each ... -
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 ... -
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 ... -
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 ... -
Molecular modeling and characterization of Vibrio cholerae transcription regulator HlyU
(BIOMED CENTRAL, 2006-11-20)Background: The SmtB/ArsR family of prokaryotic metal-regulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of heavy metal ions, while derepression results from ... -
Structural and functional characterization of soxW-a thioredoxin involved in the transport of reductants during sulfur oxidation by the global sulfur oxidation reaction cycle
(Research Journal of Microbiology, 2010)Microbial oxidation-reduction reactions involving inorganic sulfur compounds, mainly the sulfur anions, are one of the vital reactions responsible for the environmental sulfur balance. These reactions are carried out by ... -
Reinvestigating the codon and amino acid usage of S. cerevisiae genome: A new insight from protein secondary structure analysis
(ELSEVIER SCIENCE, 2003-03-28)Genomic GC (overall G + C content of the coding sequences) variations were reinvestigated between the orthologous genes of Mycobacterium tuberculosis and Mycobacterium leprae species. It was observed that overall genomic ... -
Structural study of two proteins SigE and ORF1 to predict their roles in the biochemical oxidation of sulfur anions via the global sulfur oxidation operon (sox)
(ELSEVIER SCIENCE, 2006-06)Microbial redox reactions involving inorganic sulfur compounds in the environment are one of the major reactions of the global sulfur cycle. These reactions are mediated by phylogenetically diverse prokaryotes containing ... -
Temperature adaptation of synonymous codon usage in different functional categories of genes: A comparative study between homologous genes of Methanococcus jannaschii and Methanococcus maripaludis
(ELSEVIER SCIENCE, 2006-07-10)Synonymous codon usage of homologous sequences between Methanococcus jannaschii and Methanococcus maripaludis have been analyzed in three broad functional categories of genes namely: (i) information storage and processing; ... -
Nature of selective constraints on synonymous codon usage of rice differs in GC-poor and GC-rich genes
(ELSEVIER, 2007-10-01)Synonymous codon usage and cellular tRNA abundance are thought to be co-evolved in optimizing translational efficiencies in highly expressed genes. Here in this communication by taking the advantage of publicly available ... -
Synonymous codon usage in different protein secondary structural classes of human genes: Implication for increased non-randomness of GC(3) rich genes towards protein stability
(INDIAN ACAD SCIENCES, 2007-08)The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was ...