Protip Basu

Intelligent Access to Sequence and Structure Databases (IASSD) − an interface for accessing information from major web databases

With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. Availability The Jar file is freely available through e-mail from the corresponding author.

Lysine richness in human snurps - possible sites for electrophilic attacks.

Gene-expression strategies are remodeled following exposure to stress. The reactive oxidants and electrophiles generated after stress actually affects the structural and functional properties of different cellular proteins. It is also seen that lysine rich motifs of proteins play crucial role in electrophilic attack and modification. Therefore, this study revealing lysine richness in 5 main human snrups (Small Nuclear Ribonucleoproteins) indicates a possible mechanism of gene regulation under stress. This possibility is highly supported by the findings that surface residues of the molecules were full of lysine rich clusters. Lysine richness is also found to be a highly conserved pattern across the various domains of life indicative of stress adaptation in the prebiotic to biotic world transition. Moreover the modeled structures showed good all atom contacts and minimal outliers.

Identification of conserved regulatory motif signatures in human miRNA upstream regions

Discovering and characterizing regulatory elements of miRNA genes are fundamental problems in bioinformatics field. An upstream regulatory motif can be described as a sequence element designated for binding of various protein factors imparting their subsequent effects on the transcription of the genes. For example, the transcription factors often bind to cis-acting conserved motif to regulate transcription, which typically are located upstream of transcriptional start sites. This work focuses on the identification of upstream regulatory elements of human microRNA genes by screening of their Kullback Liebler distance.

In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase.

This article has been withdrawn from the public domain because of significant plagiarism. In the light of this situation, BioMed Central regrets that this article is no longer available. The authors apologise to all affected parties for the inconvenience.

Structural and Functional analysis of glutathione peroxidase from Ricinus communis L. - a computational approach.

Oxidative stress in plants causes the induction of several enzymes, including superoxide dismutase (EC 1.15.1.1), ascorbate peroxidase (EC 1.11.1.11) and glutathione reductase (EC 1.6.4.2). The first two are responsible for converting superoxide to H2O2 and its subsequent reduction to H 2O, and the third is involved in recycling of ascorbate. Glutathione peroxidases (GPXs, EC 1.11.1.9) are a family of key enzymes involved in scavenging oxyradicals in animals. Only recently, indications for the existence of this enzyme in plants were reported. Genes with significant sequence homology to one member of the animal GPX family, namely phospholipid hydroperoxide glutathione peroxidase (PHGPX), were isolated from several plants. In this paper we report the homology modelling of the glutathione peroxidase protein from Ricinus communis L. and its interactions with its two substrates hydrogen peroxide and glutathione. Specific sites of interaction were identified and ligand binding pockets were also screened.

Genome wide snRNP motifs and regulatory sequences in HIV1 isolates

Abstract- The pathogenesis of HIV-1 is complex and characterized by the interplay of both viral and host factors. Within HIV 1 genome there are several snRNP motifs responsible for pre mRNA splicing and stabilization. By locating these motifs within the genome and disturbing them may result in an impaired ability of the cells to sustain HIV-1 replication. One of such regulatory sequences is riboswitches that regulate the dimerization of HIV-1 RNA, which is an essential step during packaging. The current work was undertaken to identify possible regulatory RNA motifs in the HIV1 genome from different isolates. The current work has successfully identified multiple snRNP motifs in the genome sequences of different strains of HIV-1 isolates. The identification of the multiple snRNP motifs in the genomic sequences of the various isolates lead us to believe that future studies with artificially constructed snRNPs might have the potential to inhibit HIV1 replication. Apart from containing snRNP motifs they also possess regulatory riboswitch motifs. Riboswitches bind metabolites and control the dimerization and packaging of the genome. Thus the occurrence of such motifs further strengthens the idea that apart from serving as a regulatory domain for structural constraints such motifs may also regulate genome integration and production of the necessary products by using the host transcriptional machinery. It is however beyond doubt that such sequence motifs must have originated in the RNA world as they have the power to mediate RNA induced regulation of gene expression.