International Journal for Computational Biology (IJCB)
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Comparative Analysis of Inter residue Contact Energy Potentials with Surrounding Hydrophobicity Model
Get PDFDuring the process of protein folding, the regular secondary structures are formed through backbone hydrogen bonding and the side chain interact each other as well as the surrounding medium to create the more complex tertiary structure. Covalent interactions between cysteine groups, non-covalent electrostatic interactions between polar groups and van-der waals interactions between non-polar groups are commonly observed in tertiary structures. To explore the role of various forces contributing to protein stability, models based on inter-residue interactions are an attractive choice. Hence, in the present work, inter residue contact energy statistical potentials are derived and related with the surrounding hydrophobicity model. Also, the statistical potentials derived by various leading research groups are also compared with the classical surrounding hydrophobicity model. Our analysis revealed the importance of hydrophobicity as a dominant force in the protein folding process
Structural Bioinformatics and Big Data Analytics: A mini-review
Get PDFStructural Biology and Structural Bioinformatics are two complementary areas that deal with three dimensional structures of biomolecules. With the advent of high-throughput techniques and automation of identifying structures there is a barrage of data generated currently, which fall under the area of Big Data. In this review, we present examples and current approach to handle massive volume of structural data and some potential applications of Big Data from Structural Bioinformatics perspective.
In-silico design of an Epitope-based peptide vaccine: A Computational Biology Approach
Get PDFLymphocytic choriomeningitis, is a rodent-borne viral infectious disease caused by Lymphocytic choriomeningitis virus (LCMV), a member of the family Arenaviridae, that was initially isolated in 1933. Acquired postnatal infection ranges from asymptomatic to a brief, nonspecific flu-like illness to critical self-resolving neurological disease, predominantly consisting of aseptic meningitis or meningoencephalitis. This study was undertaken to design an epitope-based peptide vaccine against Lymphocytic choriomeningitis virus using a computational biology approach. Twenty four sequences of LCMV were retrieved from UniProt database and analyzed with various in silico tools. VaxiJen was used to identify immunogenic peptides and T-cell epitopes were analysed using NetCTL server to identify T-cell epitopes. Out of 15 immunogenic peptides analysed using NetCTL server, a conservancy of 64.28% amongst all epitopes was observed. The peptide sequence VVQNLDQLY, a non-allergen, was found to be a potent T-cell epitope that interacted with 28 human leukocyte antigens (HLAs) and its interaction with HLA-A*02:06 was studied using protein-protein docking analysis. The HLA allele and the epitope VVQNLDQLY were found to effectively interact with each other and this epitope may be used as a vaccine against LCMV. Thus immunoinformatics based approaches can be used to predict vaccine candidates against pathogens in a timely manner and usher us into an era of T-cell based novel vaccinomics approach
Insilico drug designing and Lead Compound validation against YycG histidine kinase
No full textIn bacteria, signal transduction in response to a wide variety of environmental stimuli is mediated by pairs of proteins that communicate with each other through a two-component signal transduction system (TCS) involving protein phosphorylation. TCS consists of a histidine kinase and a response regulator, which play global roles in bacterial growth as well as drug-resistance, virulence, biofilm formation, and regulation of receptors of plant hormones such as ethylene and cytokinine. TCSs are attractive antimicrobial targets considering various prospects. YycG/YycF which is highly conserved and specific to low G +C Gram positive bacteria, are essential for Bacillus subtilis and Staphylococcus aureus survival. Inhibitors of YycG histidine kinase, such as aranorosinol B, thiazolidinone, isothiazolone etc have been screened and documented against Bacillus subtilus. This prompted us to demonstrate that S. epidermidis possesses a homologous YycG/YycF TCS, and to investigate whether it would be an appropriate target for the design of novel antibacterial agents. In our study, these novel inhibitors ZINC00518229 (GLN299:HE22), ZINC0387112 (GLN229: HE22), ZINC00014168 (HIS466:HD1), ZINC13377075 (HIS466:HD1) of YycG histidine kinase show interaction with active site residues and are considered as promising lead-compounds for developing new compounds against staphylococci infections
Nonparametric statistical test approaches in genetics data
Get PDFThe biggest challenge of genetic research lies in significant and intellectual analysis of the large and complex data sets generated by the cutting edge techniques like massively parallel DNA sequencing and genome wide analysis. Statistical analyses are the most important of such experimental data. When the data are not normally distributed and using non numerical (rank, categorical) data then use the nonparametric test for exact result of research hypothesis. Order statistics are among the most fundamental tools in non-parametric statistics and inference. Non parametric test does not depend upon parameters of the population from which the samples are drawn, no strict assumption about the distribution of the population. Nonparametric tests are known as distribution free test also because their assumptions are less and weaker than those connected with parametric test. Nonparametric test does not follow probability distribution. To analyze microarrays and genomics data several non-parametric statistical techniques are used like Wilcoxon’s signed rank test (pre-post group),Mann-Whitney U test (two groups) or Kruskal-Wallis test (two or more groups).Importance of this paper is to look at the nonparametric test how to use in genetic research and provide the understanding of these test
Development of a New Pipeline for Identification and Characterization of Micro RNAs from Plants
Get PDFOpen source microRNA analysis pipelines for next generation sequencing data (NGS) often make necessary use and working knowledge of command line interface, massive data processing resources and expertise which is a daunting task for biologists. Further, the microRNA data generated from NGS platforms will not be in a form from which one could understand or make use of it. Hence a comprehensive pipeline has been developed by integrating several open source NGS tools along with a graphical user interface called sRNAbench. It is used for expression profiling of small RNAs and prediction of microRNAs from NGS data. The pipeline features functionalities such as read processing, sequence identification, target prediction and enrichment analysis. It provides even prediction of novel microRNAs and its sequences. The pipeline will be very useful for plant genomics community and it does not require knowledge in computational biology in order to discover miRNAs and utilize the same in genomics studies
Potential interaction between presenilin and metacaspase on the Mechanism of Programed Cell Death in Leishmania infantum.
Get PDFProteases have been considered as promising targets for anti-parasitic agents, these enzymes occur in all organisms from prokaryotes to eukaryotes to viruses. The aim of the present study was to provide, through bioinformatics techniques, potential promising targets related to the apoptosis mechanism, in order to develop a vaccine and new anti-parasitic drugs.For the identifying of the hydrophobic regions, the Kyte and Doolittle methodology was utilized. The nine hydrophobic regions identified in the presenilin, based on the physicochemical properties, suggested the occurrence of transmembrane regions that were confirmed as helices scattered in the membrane by THMM. In the metacaspase structure of L. chagasi, besides the occurrence of four hydrophobic regions, the THMM analyses predicted just one helix, placed in the N-terminal portion. The analyzes of hydrophilicity through B-EpiPred Server, indicated the occurrence of several residues localized in external regions, showing that both molecules have significant numbers of fragments with high antigenic propensity. The prediction of epitopes on the tertiary structure was obtained by the I-TASSER server.In the present paper we are suggesting potential availability of a hybrid peptide originated from the presenilin and metacaspase of the Leishmania for the developing of new drugs or vaccine
In silico docking analysis of actinobacterial sideromycins with the alanine racemase enzyme of Acinetobacter baumanii
Get PDFAcinetobacter baumannii is opportunistic Gram-negative bacterial pathogen which causes hospital-acquired infections. Existence of numerous antibiotic-resistant strains of A. baumanii emphasizing the need for the development of new antimicrobials to combat them. Alanineracemase (Alr) is a pyridoxal 5'-phosphate dependent enzyme present in A. baumanii is responsible for racemization between enantiomers of alanine. As D-alanine is an essential component of the bacterial cell wall, its inhibition is lethal to prokaryotes, making it an excellent antibiotic drug target. The structure of AlrAba provides the template required for future structure-based drug-design. In this study, insilico docking studies of the sideromycins albomycin and salmycin against alanineracemase was performed. The binding energy and docked poses evaluation enabled us to conclude that the sideromycins could serve as potential inhibitor of alanine racemase which would be useful in the fight against A. baumanii.
Bourbon: Is it infectious?
Get PDFA mysterious anguish that leads to mortality of a farmer in Kansas, US on February 25th, 2015 has implicated a rise of an another deadly virus after the impact of enigmatic sufferings from Ebola called the Bourbon Virus as reported by Vox media on February 25th, 2015, though the virus was identified in 2014