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    1 OF 30

    Insights from the analysis of alginate lyase protein model from Pseudomonas fluorescens towards the understanding of mucoid biofilm disruption.
    Bioinformation 2017 30;13(9):318-322. Epub 2017 Sep 30.
    Centre for Computational Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda 151001, India.
    Bacterial biofilm is a protective, slippery and slimy coat secreted by bacterial cells. It helps in attaching to moisturized surfaces during colonization. Alginate is an important component as it is essential for retention of water and nutrients in biofilms. Read More

    Use of a neural network to predict normalized signal strengths from a DNA-sequencing microarray.
    Bioinformation 2017 30;13(9):313-317. Epub 2017 Sep 30.
    Department of Computer Science.
    A microarray DNA sequencing experiment for a molecule of N bases produces a 4xN data matrix, where for each of the N positions each quartet comprises the signal strength of binding of an experimental DNA to a reference oligonucleotide affixed to the microarray, for the four possible bases (A, C, G, or T). The strongest signal in each quartet should result from a perfect complementary match between experimental and reference DNA sequence, and therefore indicate the correct base call at that position. The linear series of calls should constitute the DNA sequence. Read More

    Analysis of predicted B and T-cell epitopes in Der p 23, allergen from Dermatophagoides pteronyssinus.
    Bioinformation 2017 30;13(9):307-312. Epub 2017 Sep 30.
    Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences-International Campus (IC-TUMS) Tehran, Iran.
    House dust mite (HDM) allergy is the leading cause of IgE-mediated hypersensitivity. Therefore identifying potential epitopes in the Dermatophagoide pteronyssinus 23 (Der p 23), a major house dust mite allergen will aid in the development of therapeutic vaccines and diagnostic kits for HDM allergy. Experimental methods of epitope discovery have been widely exploited for the mapping of potential allergens. Read More

    Prediction aided in vitro analysis of octa-decanoic acid from Cyanobacterium Lyngbya sp. as a proapoptotic factor in eliciting anti-inflammatory properties.
    Bioinformation 2017 30;13(9):301-306. Epub 2017 Sep 30.
    Department of Microbiology, Bharathidasan University, Tiruchirappalli - 620024, Tamilnadu, India.
    Marine Lyngbya has been proven as a potent anticancer agent by disrupting microfilament network. Lyngbya and its associated cyanobacterial compounds have been stressed for futuristic advancements in cancer research and have foreseen explicit advancements in the recent era. Moreover, compounds like lyngbyabellins, lyngbyastatins and other derived toxins are significantly studied. Read More

    Molecular docking analysis of aplysin analogs targeting survivin protein.
    Bioinformation 2017 30;13(9):293-300. Epub 2017 Sep 30.
    Advanced Centre for Bioengineering and Bioinformatics (ACBB), Integral Information and Research Centre (IIRC), Integral University, Lucknow, Uttar Pradesh, India-226026.
    Survivin (IAP proteins) remains an important target for anticancer drug development as it is reported to be over-expressed in tumor cells to enhance resistance to apoptotic stimuli. The study focuses on virtual screening of marine compounds inhibiting survivin, a multifunctional protein, using a computational approach. Structures of compounds were prepared using ChemDraw Ultra 10. Read More

    Molecular docking based screening of triterpenoids as potential G-quadruplex stabilizing ligands with anti-cancer activity.
    Bioinformation 2017 30;13(9):284-292. Epub 2017 Sep 30.
    Department of Pharmacology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Bangkok 10400, Thailand.
    Triterpenoids isolated from Ganoderma lucidum (GLTs) exhibit a broad spectrum of anti-cancer properties, including anti-proliferative, anti-metastatic and anti-angiogenic activities. Current research studies revealed the role by GLTs in inducing apoptosis and suppression of telomerase activity of cancer cells with much lower toxicity to healthy cells. Compounds selectively binding and stabilizing G-quadruplex structures could inhibit the telomerase or downregulate the oncogenes and may act as anti-cancer agents. Read More

    Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent.
    Bioinformation 2017 30;13(9):274-283. Epub 2017 Sep 30.
    Durga Femto Technologies and Research, Bangalore 560018, Karnataka, India.
    Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Read More

    Potential Hemoglobin A/F role in clinical Malaria.
    Bioinformation 2017 31;13(8):269-273. Epub 2017 Aug 31.
    Immunology Division, ICMR-National Institute of Malaria Research, Dwarka, New Delhi; Present Address: Regional Medical Research Centre, Belagavi, Nehru Nagar, National Highway No.4, Belagavi-590010, Karnataka, India.
    The Malarial parasite resides in the host RBC during its erythrocytic cycle. Plasmodium meets its entire nutritional requirement from RBC. It scavenges the hemoglobin of RBCs to meet its amino acid requirement. Read More

    Druggability and Binding Site Interaction Studies of Potential Metabolites Isolated from Marine Sponge Aurora globostellata against Human Epidermal Growth Factor Receptor-2.
    Bioinformation 2017 31;13(8):261-268. Epub 2017 Aug 31.
    Centre for Drug Discovery and Development, Jeppiaar Research park, Sathyabama University, Chennai 600119,Tamilnadu, India.
    To study the involvement of compounds stigmasterol and oleic acid isolated from marine sponge Aurora globostellata and docking against the Human Epidermal Growth Factor Receptor-2 in breast cancer. The comparative molecular docking was performed with the natural compounds from marine sponge and the synthetic drugs used in breast cancer treatment against the target HER2. The molecular docking analysis was done using GLIDE in Schrodinger software package. Read More

    Marine sponge derived natural products as inhibitors of mycothiol-S-conjugate amidase.
    Bioinformation 2017 31;13(8):256-260. Epub 2017 Aug 31.
    School of Biotechnology, IFTM University, Lodhipur Rajput, Delhi Road, Moradabad 244001, U.P., India.
    Marine sponges have potential sources for secondary metabolites and are considered as a drug treasure house. In this work, 3D model of Mycothiol-S-conjugate amidase (Mca) was determined by comparative homology modeling program MODELLER based on the crystal structure of 1-D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) from Mycobacterium tuberculosis as a template. The computed model's energy was minimized and validated to obtain a stable model structure. Read More

    Identification of long non-coding RNA in rice lines resistant to Rice blast pathogen Maganaporthe oryzae.
    Bioinformation 2017 31;13(8):249-255. Epub 2017 Aug 31.
    ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi-110012, India.
    Rice blast disease caused by a fungus Magnaporthae oryzae is one of the most important biotic factors that severely damage the rice crop. Several molecular approaches are now being applied to tackle this issue in rice. It is of interest to study long non-coding RNA (lncRNA) in rice to control the disease. Read More

    Naturally occurring capsid protein variants L1 of human papillomavirus genotype 16 in Morocco.
    Bioinformation 2017 31;13(8):241-248. Epub 2017 Aug 31.
    Unit of Biology and Medical Research, National Centre Natuional de l´Energie, des Sciences et des techniques Nucléaires. Morocco.
    HPV L1 protein is a corner stone in HPV structure, it's involved in the formation of the viral capsid; widely used as a systematic material and considered as the main component in vaccines development and production. The present study aims to characterize genetic variation of L1 gene of HPV 16 specimens and to evaluate in silico the impact of major variants on the epitope change affecting its conformational structure. A fragment of L1 gene from 35 HPV 16 confirmed specimens were amplified by PCR and sequenced. Read More

    Docking analysis of verteporfin with YAP WW domain.
    Bioinformation 2017 31;13(7):237-240. Epub 2017 Jul 31.
    Laboratoire de Biotechnologie (MedBiotech), Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Rabat, Morocco.
    The YAP oncogene is a known cancer target. Therefore, it is of interest to understand the molecular docking interaction of verteporfin (a derivative of benzo-porphyrin) with the WW domain of YAP (clinically used for photo-dynamic therapy in macular degeneration) as a potential WW domain-ligand modulator by inhibition. A homology protein SWISS MODEL of the human YAP protein was constructed to dock (using AutoDock vina) with the PubChem verteporfin structure for interaction analysis. Read More

    Short peptide epitope design from hantaviruses causing HFRS.
    Bioinformation 2017 31;13(7):231-236. Epub 2017 Jul 31.
    Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu, India.
    Several genotypes of the hantavirus cause hemorrhagic fever with renal syndrome (HFRS) and is an important public health problem worldwide. There is now growing interest to develop subunit vaccines especially focused to elicit cytotoxic T lymphocyte responses which are important against viral infection. We identified candidate T-cell epitopes that bind to Class I HLA supertypes towards identifying potential subunit vaccine entity. Read More

    A Genomic Signature for Genotyping Mycobacterium tuberculosis.
    Bioinformation 2017 31;13(7):224-230. Epub 2017 Jul 31.
    Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú.
    Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has a vast diversity of genotypes including Beijing, CAS, EAI, Haarlem, LAM, X, Ural, T, AFRI1 and AFRI2. However, genotyping can be expensive, time consuming and in some cases, results may vary depending on methodology used. Here, we proposed a new set of 10 SNPs using a total of 249 MTB genomes, and selected by first the inclusion/ exclusion (IE) criteria using spoligotyping and phylogenies, followed by the selection of the nonsynonymous SNPs present in the most conserved cluster of orthologous groups (COG) of each genotype of MTB. Read More

    Designing Epitope Ensemble Vaccines against TB by Selection: Prioritizing Antigens using Predicted Immunogenicity.
    Bioinformation 2017 31;13(7):220-223. Epub 2017 Jul 31.
    School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, United Kingdom, B4 7ET.
    Tuberculosis (TB) is a global health burden, and a major cause of mortality and morbidity in West Africa. Here, we select key conserved pathogen epitopes of proven immunogenicity to form a potential TB epitope ensemble vaccine. We compared two vaccine formulations: one comprising class I epitopes from the 13 most prevalent class I epitope-bearing antigens and class II epitopes deriving from the 20 most prevalent class II epitope-bearing antigens and another consisting of epitopes derived solely from 5 antigens identified as the most immunogenic by VaxiJen. Read More

    Meta-analysis study to evaluate the association of MTHFR C677T polymorphism with risk of ischemic stroke.
    Bioinformation 2017 30;13(6):214-219. Epub 2017 Jun 30.
    Department of Bioinformatics, Sri Ramachandra University, Porur, Chennai-600 116, India.
    Ischemic stroke is a condition characterized by reduced blood supply to part of the brain, initiating the ischemic cascade, leading to dysfunction of the brain tissue in that area. It is one of the leading causes of death and disability and is estimated to cause around 5.7 million deaths worldwide. Read More

    Deciphering the Role of microRNAs in BRD4-NUT Fusion Gene Induced NUT Midline Carcinoma.
    Bioinformation 2017 30;13(6):209-213. Epub 2017 Jun 30.
    Bioinformatics Department, MMV, Banaras Hindu University, India.
    NUT midline carcinoma (NMC) is a very aggressive and lethal type of squamous epithelial cell cancer caused due to fusion of BRD4 and NUT genes. The gene fusion results into a new fusion protein that promotes oncogenesis. The detailed molecular mechanisms underlying the NMC are still not clear and new findings are urgently required to complement the current efforts. Read More

    Serum and Plasma Metabolomic Biomarkers for Lung Cancer.
    Bioinformation 2017 30;13(6):202-208. Epub 2017 Jun 30.
    Bioinformatics Lab, Department of Statistics, Rajshahi University, Rajshahi, Bangladesh.
    In drug invention and early disease prediction of lung cancer, metabolomic biomarker detection is very important. Mortality rate can be decreased, if cancer is predicted at the earlier stage. Recent diagnostic techniques for lung cancer are not prognosis diagnostic techniques. Read More

    Combination of bone marrow mesenchymal stem cells and cartilage fragments contribute to enhanced repair of osteochondral defects.
    Bioinformation 2017 30;13(6):196-201. Epub 2017 Jun 30.
    Department of Orthopaedic Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.
    Cartilage tissue engineering using stem cells and biomaterials is considered a promising approach despite poor outcomes. We hypothesise that articular cartilage fragments provides native environmental cues to enhance stem cell differentiation. As such we evaluated the chondrogenic differentiation and repair of critical size defect in a human explant osteochondral model (OD) using bone marrow derived mesenchymal stem cells (BM-MSCs) and homogenised cartilage. Read More

    Designing of a penta-peptide against drug resistant E. coli.
    Bioinformation 2017 30;13(6):192-195. Epub 2017 Jun 30.
    Department of Biotechnology, Maharishi Markandeshwar University, Mullana, Ambala, haryana 133207.
    Drug resistant pathogens are vibrant global problem. Penicillin binding protein 5 (PBP5) plays important role in bacterial cell wall biosynthesis. Mutation in PBP5 is a well-known mechanism for development of drug resistant strain of bacteria. Read More

    Structural insight into the binding of C60-derivatives with enoyl-pyruvate transferase from Helicobacter pylori.
    Bioinformation 2017 30;13(6):185-191. Epub 2017 Jun 30.
    Department of Biochemistry, Huazhong University of science and Technology, China.
    Helicobacter pylori (H. pylori) is a human pathogen associated with acute gastritis and peptic ulcer. The MurA enzyme is an important drug target for the identification of ligands with improved efficacy and acceptable pharmaco-kinetic properties. Read More

    Transcriptome wide identification and characterization of starch branching enzyme in finger millet.
    Bioinformation 2017 30;13(6):179-184. Epub 2017 Jun 30.
    Uttarakhand Technical University, Dehradun, Uttarakhand, 248007, India.
    Starch-branching enzymes (SBEs) are one of the four major enzyme classes involved in starch biosynthesis in plants and play an important role in determining the structure and physical properties of starch granules. Multiple SBEs are involved in starch biosynthesis in plants. Finger millet is calcium rich important serial crop belongs to grass family and the transcriptome data of developing spikes is available on NCBI. Read More

    Analysis of correlated mutations in Ras G-domain.
    Bioinformation 2017 30;13(6):174-178. Epub 2017 Jun 30.
    Bioinformatics Department, MMV, Banaras Hindu University.
    Ras GTPases are most prevalent proto-oncogenes in human cancer. Mutations in Ras remain untreatable more than three decades after the initial discovery. At the amino acid level, some residues under physical or functional constraints exhibit correlated mutations also known as coevolving/covariant residues. Read More

    Protein-protein interfaces are vdW dominant with selective H-bonds and (or) electrostatics towards broad functional specificity.
    Bioinformation 2017 30;13(6):164-173. Epub 2017 Jun 30.
    Biomedical Informatics (P) Ltd, Irulan Sandy Annex, Puducherry 607 402, India.
    Several catalysis, cellular regulation, immune function, cell wall assembly, transport, signaling and inhibition occur through Protein- Protein Interactions (PPI). This is possible with the formation of specific yet stable protein-protein interfaces. Therefore, it is of interest to understand its molecular principles using structural data in relation to known function. Read More

    Molecular docking based screening of Listeriolysin-O for improved inhibitors.
    Bioinformation 2017 31;13(5):160-163. Epub 2017 May 31.
    Vira Vigene research institute, Tehran, Iran.
    Listeriolysine-O (LLO) is a 50KDa protein responsible for Listeria monocytogenes pathogenicity. The structure of LLO (PDB ID: 4CDB) with domains D1 to D4 is known. Therefore, it is of interest to identify conserved regions among LLO variants for destabilizing oligomerization (50 mer complex) of its monomers using appropriate inhibitors. Read More

    QSAR based predictive modeling for anti-malarial molecules.
    Bioinformation 2017 31;13(5):154-159. Epub 2017 May 31.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-67.
    Malaria is a predominant infectious disease, with a global footprint, but especially severe in developing countries in the African subcontinent. In recent years, drug-resistant malaria has become an alarming factor, and hence the requirement of new and improved drugs is more crucial than ever before. One of the promising locations for antimalarial drug target is the apicoplast, as this organelle does not occur in humans. Read More

    Polymorphism of the PAI-1gene (4G/5G) may be linked with Polycystic Ovary Syndrome and associated pregnancy disorders in South Indian Women.
    Bioinformation 2017 31;13(5):149-153. Epub 2017 May 31.
    Genes N Life Healthcare, Hyderabad.
    Polycystic Ovary syndrome (PCOS) is the most common endocrine disorder affecting 5 - 10% of all women of reproductive age group. The present research was carried out to study the impact of Plasminogen Activator Inhibitor (PAI-1) 4G/5G polymorphism (rs1799889) in PCOS, and the risk of developing PCOS in South Indian Population. The study was carried out in 60 subjects of South Indian population (30 PCOS and 30 Non PCOS) recruited from ARC Research and Fertility Centre, Chennai, India. Read More

    Identification of inhibitors against α-Isopropylmalate Synthase of Mycobacterium tuberculosis using docking-MM/PBSA hybrid approach.
    Bioinformation 2017 31;13(5):144-148. Epub 2017 May 31.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, INDIA 110067.
    α-Isopropylmalate Synthase (α-IPMS) encoded by leuA in Mycobacterium tuberculosis (M.tb) is involved in the leucine biosynthesis pathway and is extremely critical for the synthesis of branched-chain amino acids (leucine, isoleucine and valine). α-IPMS activity is required not only for the proliferation of M. Read More

    Competitive rational inhibitor design to 4-maleylaceto-acetate isomerase.
    Bioinformation 2017 31;13(5):140-143. Epub 2017 May 31.
    National institute of genetic engineering and biotechnology, Tehran, Iran.
    Tyrosinemia type I is the result of genetic disorder in fomaryl acetoacetase gene that leads to 4-fumaryl acetoacetate accumulation. The current treatment for tyrosinemia type I is nitisinone that inhibits 4-hydroxyphenyl pyruvic dioxygenase in competitive manner. In the present study, we have designed two theoretical chemicals, which could inhibit the direct enzyme responsible for fumarylacetoacetate formation. Read More

    Molecular docking analysis of nitisinone with homogentisate 1,2 dioxygenase.
    Bioinformation 2017 31;13(5):136-139. Epub 2017 May 31.
    National institute of genetic engineering and biotechnology, Tehran, Iran.
    Alkaptonuria is an inherited disease that is caused by homogenticate accumulation. Deficiency or mutation in Homogentisate 1,2 dioxygenase gene (chromosome 3q21-q23) leads to production of incorrectly folded or truncated enzyme. Several studies indicated that competitive inhibitors of Homogentisate 1,2 dioxygenase like Nitisinone could be used for Alkaptonuria treatment. Read More

    Dengue Symptoms Significance in Anti-Dengue Drug Development: Road Less Travelled.
    Bioinformation 2017 31;13(5):131-135. Epub 2017 May 31.
    SRM University, Delhi-NCR, Sonepat, Haryana, Centre for Drug Design Discovery & Development (C-4D), PR Institute of Medical Science & Research, Delhi-NCR, Sonepat, New Delhi, India.
    Dengue outbreak has affected rural areas of Delhi-NCR, Haryana widely but it lacks in surveillance. High cases of dengue symptoms were reported in these regions whereas dengue symptoms have been a neglected issue in the anti-dengue drug development. Therefore, this study aims to analyze the status of the dengue infection, a rural issue of Delhi-NCR, Haryana and to identify the significance of dengue symptoms in anti-dengue drug development. Read More

    Linear epitope prediction in HPV type 16 E7 antigen and their docked interaction with human TMEM 50A structural model.
    Bioinformation 2017 31;13(5):122-130. Epub 2017 May 31.
    Department of Computer Science and Information Technology, Sam Higginbottom Institute of Agriculture, Technology and Sciences, Allahabad-211007, India.
    Human Papilloma Virus (HPV) HPV type 16 E7 antigen is a known target in cervical cancer. We report the predicted potential epitopes in the E7 antigen. We further describe the subsequent interaction of these linear epitope peptides with the human TMEM 50 A structural model using molecular docking. Read More

    Nucleotide composition determines the role of translational efficiency in human genes.
    Bioinformation 2017 28;13(2):46-53. Epub 2017 Feb 28.
    Department of Biotechnology, Assam University, Silchar-788011, Assam, India.
    The basic sequence features were analysed that influence gene expression via codon usage bias of the selected forty coding sequences of Homo sapiens in a simple prokaryotic model i.e. E. Read More

    Virtual screening following rational drug design based approach for introducing new anti amyloid beta aggregation agent.
    Bioinformation 2017 28;13(2):42-45. Epub 2017 Feb 28.
    Viravigene research institute, Tehran, Iran.
    Amyloid β (Aβ) sheets aggregations is the main reason of Alzheimer disease. The interacting areas between monomers are residue number 38 to 42. Inhibition of interaction between Aβ molecules prevents plaque formation. Read More

    Analysis of MAP kinase MPK4/MEKK1/MKK genes of Carica papaya L. comparative to other plant homologues.
    Bioinformation 2017 28;13(2):31-41. Epub 2017 Feb 28.
    Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
    Mitogen-activated protein kinase 4 (MPK4) interacts with the (Mitogen-activated protein kinase kinase kinase 1) MEKK1/ Mitogenactivated protein kinase kinase 1 (MKK1)/ Mitogen-activated protein kinase kinase 2 (MKK2) complex to affect its function in plant development or against pathogen attacks. The KEGG (Kyoto Encyclopedia of Genes and Genomes) network analysis of Arabidopsis thaliana revealed close interactions between those four genes in the same plant-pathogen interaction pathway, which warrants further study of these genes due to their evolutionary conservation in different plant species. Through targeting the signature sequence in MPK4 of papaya using orthologs from Arabidopsis, the predicted sequence of MPK4 was studied using a comparative in silico approach between different plant species and the MAP cascade complex of MEKK1/MKK1/MKK2. Read More

    optCluster: An R Package for Determining the Optimal Clustering Algorithm.
    Bioinformation 2017 31;13(3):101-103. Epub 2017 Mar 31.
    Department of Biostatistics, University of Florida, Gainesville, Florida, 32611, USA.
    There exist numerous programs and packages that perform validation for a given clustering solution; however, clustering algorithms fare differently as judged by different validation measures. If more than one performance measure is used to evaluate multiple clustering partitions, an optimal result is often difficult to determine by visual inspection alone. This paper introduces optCluster, an R package that uses a single function to simultaneously compare numerous clustering partitions (created by different algorithms and/or numbers of clusters) and obtain a "best" option for a given dataset. Read More

    T-cell epitopes predicted from the Nucleocapsid protein of Sin Nombre virus restricted to 30 HLA alleles common to the North American population.
    Bioinformation 2017 31;13(3):94-100. Epub 2017 Mar 31.
    Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore 632 055, Tamil Nadu,India.
    Hantavirus cardiopulmonary syndrome in North America is caused by Sin Nombre virus (SNV) and poses a public health problem. We identified T-cell epitopes restricted to HLA alleles commonly seen in the N. American population. Read More

    Epitope design of L1 protein for vaccine production against Human Papilloma Virus types 16 and 18.
    Bioinformation 2017 31;13(3):86-93. Epub 2017 Mar 31.
    Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Chittagong 4202, Bangladesh.
    Cervical cancer accounts for about two-thirds of all cancer cases linked etiologically to Human Papilloma Virus (HPV). 15 oncogenic HPV types can cause cervical cancer, of which HPV16 and HPV18 combinedly account for about 70% of it. So, effective epitope design for the clinically relevant HPV types 16 and 18 would be of major medical benefit. Read More

    Identification and characterization of a cyclosporin binding cyclophilin from Staphylococcus aureus Newman.
    Bioinformation 2017 31;13(3):78-85. Epub 2017 Mar 31.
    Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India.
    Cyclophilins, a class of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes, are inhibited by cyclosporin A (CsA), an immunosuppressive drug. Staphylococcus aureus Newman, a pathogenic bacterium, carries a gene for encoding a putative cyclophilin (SaCyp). SaCyp shows significant homology with other cyclophilins at the sequence level. Read More

    Analysis of EAWAG-BBD pathway prediction system for the identification of malathion degrading microbes.
    Bioinformation 2017 31;13(3):73-77. Epub 2017 Mar 31.
    Department of Microbiology, Sri Sankara Arts and Science College, Enathur - 631 561.
    Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and most versatile class of insecticide used and Malathion is the predominant type utilized. Read More

    Antimicrobial activity of various ethanolic plant extracts against pathogenic multi drug resistant Candida spp.
    Bioinformation 2017 31;13(3):67-72. Epub 2017 Mar 31.
    Department of Biosciences, Integral University, Lucknow U.P. India.
    A total of 50 Candida isolates were isolated and identified from clinical specimens and these were tested for resistance to various antifungal drugs. It was observed multi-drug resistance in all candida isolates by 84%, 62%, 60%, 76%, 46, 30%, and 22% against fluconazole, clotrimazole, Amphotericin B, itraconazole, ketoconazole, miconazole and nystatin tested respectively. The isolates, which were found to be resistant to antifungal drugs were selected and subjected to antifungal testing against six ethanolic plants, extract namely Azadiracta indica, Allium sativum, Cordia dichotoma Ocimum sanctum, Syzygium cumini and Trigonella foenum grecum. Read More

    A comparative molecular docking study of curcumin and methotrexate to dihydrofolate reductase.
    Bioinformation 2017 31;13(3):63-66. Epub 2017 Mar 31.
    College of Applied Medical Sciences Jazan University, Jazan, Kingdom of Saudi Arabia.
    Interaction of curcumin (CUR) with the enzyme dihydrofolate reductase (DHFR) was studied by molecular docking using AutoDock 4.2 as the docking software application. AutoDock 4. Read More

    Quantitative Structure Activity Relationship study of the Anti-Hepatitis Peptides employing Random Forests and Extra-trees regressors.
    Bioinformation 2017 31;13(3):60-62. Epub 2017 Mar 31.
    Shiv Nadar University, Gautam Budha Nagar, Uttar Pradesh 201314, India.
    Antimicrobial peptides are host defense peptides being viewed as replacement to broad-spectrum antibiotics due to varied advantages. Hepatitis is the commonest infectious disease of liver, affecting 500 million globally with reported adverse side effects in treatment therapy. Antimicrobial peptides active against hepatitis are called as anti-hepatitis peptides (AHP). Read More

    Annotation of gene sequence and protein structure of brinjal EDS1.
    Bioinformation 2017 2;13(3):54-59. Epub 2017 Mar 2.
    Division of Genomic Resources, IACR-NBPGR, Pusa Campus, New Delhi, India.
    Enhanced Disease Susceptibility1 (EDS1) is a nucleo-cytoplasmic protein, known to be a key regulator of plant basal defense and effector-triggered immunity. Sequence of a single copy brinjal EDS1 gene (SmEDS1) was mined from draft brinjal genome assembly. The extracted sequence was found to be incomplete and polished with the help of transcriptome sequence data. Read More

    Molecular Docking of Phytoligands to the viral protein receptor P. monodon Rab7.
    Bioinformation 2017 30;13(4):116-121. Epub 2017 Apr 30.
    Centre for Drug Discovery and Development, Sathyabama University, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai-600 119, Tamil Nadu, INDIA.
    The development of shrimp aquaculture has been severely affected by viral diseases resulting in a huge economic burden to the industry. White spot disease (WSD) has caused severe mortality in farmed shrimp in many countries. Globally aquaculture industries face huge economic losses due to rapid spread of White Spot Syndrome Virus (WSSV) disease that can cause 100% mortality in a short period of 3-10 days. Read More

    Influence of PCOS in Obese vs. Non-Obese women from Mesenchymal Progenitors Stem Cells and Other Endometrial Cells: An in silico biomarker discovery.
    Bioinformation 2017 30;13(4):111-115. Epub 2017 Apr 30.
    Faculty of Computing and Information Technology, King Abdul-Aziz University, Rabigh-21911, Saudi Arabia.
    Polycystic ovary syndrome (PCOS) is endocrine system disease which affect women ages 18 to 44 where the women's hormones are imbalance. Recently it has been reported to occur in early age. Alteration of normal gene expression in PCOS has shown negative effects on long-term health issues. Read More

    Improved Annotations of 23 Differentially Expressed Hypothetical Proteins in Methicillin Resistant S.aureus.
    Bioinformation 2017 30;13(4):104-110. Epub 2017 Apr 30.
    Department of Science, Davenport University, Lansing, Michigan, United States of America.
    Antibiotic resistant Staphylococcus aureus is a major public health concern effecting millions of people annually. Medical science has documented completely untreatable S. aureus infections. Read More

    Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data.
    Bioinformation 2017 31;13(1):25-30. Epub 2017 Jan 31.
    Biotechnology Research Institute for Drug Discovery, National Institute of AIST, Tokyo, Japan.
    Functional genomics and gene regulation inference has readily expanded our knowledge and understanding of gene interactions with regards to expression regulation. With the advancement of transcriptome sequencing in time-series comes the ability to study the sequential changes of the transcriptome. Here, we present a new method to augment regulation networks accumulated in literature with transcriptome data gathered from time-series experiments to construct a sequential representation of transcription factor activity. Read More

    Cloning and over expression of non-coding RNA rprA in E.coli and its resistance to Kanamycin without osmotic shock.
    Bioinformation 2017 31;13(1):21-24. Epub 2017 Jan 31.
    Nour Danesh Institute of Higher Education, Department of Biology, Isfahan, Iran.
    Recent reports have indicated that small RNAs have key roles in the response of the E.coli to stress and also in the regulating of virulence factors. It seems that some small non-coding RNAs are involved in multidrug resistance. Read More

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