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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/28660537/in-silico-analysis-of-nssnps-of-carp-tlr22-gene-affecting-its-binding-ability-with-poly-i-c
#1
Vemulawada Chakrapani, Kiran D Rasal, Sunil Kumar, Shibani D Mohapatra, Jitendra K Sundaray, Pallipuram Jayasankar, Hirak K Barman
Immune response mediated by toll-like receptor 22 (TLR22), only found in teleost/amphibians, is triggered by double-stranded RNA binding to its LRR (leucine-rich repeats) ecto-domain. Accumulated evidences suggested that missense mutations in TLR genes affect its function. However, information on mutation linked pathogen recognition for TLR22 was lacking. The present study was commenced for predicting the effect of non-synonymous single-nucleotide polymorphisms (nsSNPs) on the pathogen recognizable LRR domain of TLR22 of farmed carp, Labeo rohita...
June 28, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28660536/in-silico-identification-of-novel-micrornas-and-targets-using-est-analysis-in-allium-cepa-l
#2
Bahram Baghban Kohnehrouz, Meysam Bastami, Shahnoush Nayeri
microRNAs (miRNAs) are a newly discovered class of non-coding small RNAs roughly 22 nucleotides long. Increasing evidence has shown that miRNAs play multiple roles in biological processes, including development, cell proliferation, apoptosis and stress responses. The identification of miRNAs and their targets is an important need to understand their roles in the development and physiology of sweet onion (Allium cepa). In this research, several computational approaches were combined to make concise prediction of the potential miRNAs and their targets...
June 28, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28631174/studies-of-the-interaction-of-influenza-virus-rna-polymerase-pan-with-endonuclease-inhibitors
#3
Li-Hua Dong, Xiao-Rong Cao
Influenza virus is a major causative agent of respiratory viral infections, and RNA polymerase catalyzes its replication and transcription activities in infected cell nuclei. Since it is highly conserved in all virus strains, RNA polymerase becomes a key target of anti-influenza virus agents. Although experimental studies have revealed the good inhibitory activity of endonuclease inhibitors to RNA polymerase, the mechanism is still unclear. In this study, the docking and molecular dynamics simulations have been performed to explore the interaction of three kinds of endonuclease inhibitors with the subunit (PAN) of RNA polymerase...
June 19, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28623462/in-silico-investigations-of-chemical-constituents-of-clerodendrum-colebrookianum-in-the-anti-hypertensive-drug-targets-rock-ace-and-pde5
#4
Hemant Arya, Safiulla Basha Syed, Sorokhaibam Sureshkumar Singh, Dinakar R Ampasala, Mohane Selvaraj Coumar
Understanding the molecular mode of action of natural product is a key step for developing drugs from them. In this regard, this study is aimed to understand the molecular-level interactions of chemical constituents of Clerodendrum colebrookianum Walp., with anti-hypertensive drug targets using computational approaches. The plant has ethno-medicinal importance for the treatment of hypertension and reported to show activity against anti-hypertensive drug targets-Rho-associated coiled-coil protein kinase (ROCK), angiotensin-converting enzyme, and phosphodiesterase 5 (PDE5)...
June 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28560699/identification-of-strategic-residues-at-the-interface-of-antigen-antibody-interactions-by-in-silico-mutagenesis
#5
Lu Xin, Hai Yu, Qiyang Hong, Xingjian Bi, Xiao Zhang, Zhiqing Zhang, Zhibo Kong, Qingbing Zheng, Ying Gu, Qinjian Zhao, Jun Zhang, Shaowei Li, Ningshao Xia
Structural information pertaining to antigen-antibody interactions is fundamental in immunology, and benefits structure-based vaccine design. Modeling of antigen-antibody immune complexes from co-crystal structures or molecular docking simulations provides an extensive profile of the epitope at the interface; however, the key amino acids involved in the interaction must be further clarified, often through the use of experimental mutagenesis and subsequent binding assays. Here, we describe an in silico mutagenesis method to identify key sites at antigen-antibody interfaces, using significant increase in pH-dependency energy among saturated point mutations...
May 30, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28534166/in-silico-identification-and-validation-of-potential-micrornas-in-kinnow-mandarin-citrus-reticulata-blanco
#6
Prashant Mohanpuria, Naveen Duhan, Navraj Kaur Sarao, Manvir Kaur, Mandip Kaur
MicroRNAs (miRNAs) are a large family of 19-25 nucleotides, regulatory, non-coding RNA molecules that control gene expression by cleaving or inhibiting the translation of target gene transcripts in animals and plants. Despite the important functions of miRNAs related to regulation of plant growth and development processes, metabolism, and abiotic and biotic stresses, little is known about the disease-related miRNA. Here, we present a new pipeline for miRNA analysis using expressed sequence tags (ESTs)-based bioinformatics approach in Kinnow mandarin, a commercially important citrus fruit crop...
May 22, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28527150/development-of-in-silico-protocols-to-predict-structural-insights-into-the-metabolic-activation-pathways-of-xenobiotics
#7
M Kalim A Khan, Salman Akhtar, Jamal M Arif
To establish in silico model to predict the structural insight into the metabolic bioactivation pathway of xenobiotics, we considered two specific and one non-specific mammary procarcinogen [e.g., dibenzo[a,l]pyrene (DBP), 7,12-dimethylbenz[a]anthracene (DMBA), and benzo[a]pyrene (BP)]. The CYP1A1, 1B1, 2C9, 1A2 and 2B6 reported in wet-lab studies to actively metabolize DBP also showed strong binding energies (kcal/mol) of -11.50, -10.67, -10.37, -9.76 and -9.72, respectively, with inhibition constants ranging between 0...
May 19, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28516319/quantitative-prediction-of-drug-side-effects-based-on-drug-related-features
#8
Yanqing Niu, Wen Zhang
MOTIVATION: Unexpected side effects of drugs are great concern in the drug development, and the identification of side effects is an important task. Recently, machine learning methods are proposed to predict the presence or absence of interested side effects for drugs, but it is difficult to make the accurate prediction for all of them. METHODS: In this paper, we transform side effect profiles of drugs as their quantitative scores, by summing up their side effects with weights...
May 17, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28488219/inhibition-of-gelatinases-mmp-2-and-mmp-9-by-withania-somnifera-phytochemicals-confers-neuroprotection-in-stroke-an-in-silico-analysis
#9
Gaurav Kumar, Ranjana Patnaik
A stroke or cerebrovascular accident is a serious, life-threatening medical condition that occurs when the blood supply to part of the brain is severely reduced or cut off, depriving brain tissue of oxygen and nutrients. Studies suggested that level of gelatinases (MMP-2 and MMP-9) usually increases in the brain after stroke. The elevated activity of gelatinases plays the deleterious role in ischemic stroke, hemorrhagic stroke and perinatal hypoxic-ischemic brain injury. Therefore, matrix metalloproteinase (MMP)-2 and MMP-9 inhibition have therapeutic importance in stroke condition...
May 9, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28488218/discovery-of-therapeutic-lead-molecule-against-%C3%AE-tubulin-using-computational-approach
#10
K Ramanathan, Kanika Verma, Naina Gupta, V Shanthi
Virtual screening strategy was performed against the target β-tubulin to overcome paclitaxel resistance in blood cancer types. In essence, A185T and A248V are two such important mutations frequently observed in clinical trials that confer paclitaxel resistance. In the present investigation, compounds from NPACT database were filtered by pharmacokinetics, toxicity and binding energy values. A total of 5 active compounds were identified from a list of 1574 bioactive compounds investigated in our study. Finally, we have compiled all the characteristic features into biologically meaningful clusters by hierarchical clustering algorithm...
May 9, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28478537/micelles-rods-liposomes-and-other-supramolecular-surfactant-aggregates-computational-approaches
#11
REVIEW
Serena Indelicato, David Bongiorno, Valentina Calabrese, Ugo Perricone, Anna Maria Almerico, Leopoldo Ceraulo, Daniela Piazzese, Marco Tutone
Surfactants are an interesting class of compounds characterized by the segregation of polar and apolar domains in the same molecule. This peculiarity makes possible a whole series of microscopic and macroscopic effects. Among their features, their ability to segregate particles (fluids or entire domains) and to reduce the surface/interfacial tension is the utmost important. The interest in the chemistry of surfactants never weakened; instead, waves of increasing interest have occurred every time a new field of application of these molecules has been discovered...
May 6, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28352971/ir-spectra-of-different-o2-content-hemoglobin-from-computational-study-promising-detector-of-hemoglobin-variant-in-medical-diagnosis
#12
Su-Qin Zhou, Tu-Nan Chen, Guang-Fu Ji, En-Ren Wang
IR spectra of heme and different O2-content hemoglobin were studied by the quantum computation method at the molecule level. IR spectra of heme and different O2-content hemoglobin were quantificationally characterized from 0 to 100 THz. The IR spectra of oxy-heme and de-oxy-heme are obviously different at the frequency regions of 9.08-9.48, 38.38-39.78, 50.46-50.82, and 89.04-91.00 THz. At 24.72 THz, there exists the absorption peak for oxy-heme, whereas there is not the absorption peak for de-oxy-heme. Whether the heme contains Fe-O-O bond or not has the great influence on its IR spectra and vibration intensities of functional groups in the mid-infrared area...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28013448/change-in-glutenin-macropolymer-secondary-structure-in-wheat-sourdough-fermentation-by-ftir
#13
Jinshui Wang, Yuanyuan Yue, Tiantian Liu, Bin Zhang, Zhenlei Wang, Changfu Zhang
Wheat sourdough was prepared by fermentation with Lactobacillus plantarum M616 and yeast in the present study. The change in secondary structure of glutenin macropolymer (GMP) in wheat sourdough fermentation for 4 and 12 h was determined using Fourier transform infrared spectroscopy, and then the resultant spectra were Fourier self-deconvoluted of the amide I band in the region from 1600 to 1700 cm(-1). Significant different spectra especially in the amide I band for GMP from sourdough fermented with L. plantarum M616 (SL) and with L...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27013508/effect-of-solvent-water-molecules-on-human-serum-albumin-complex-docked-paclitaxel-by-mm-pbsa-method
#14
Huaxing Yu, Daixi Li, Fei Xu, Baolin Liu, Chenglung Chen
Molecular modeling on solvation effect and interaction mechanism of the water molecules in the active site of protein affect significantly the interaction between protein and ligand. Detailed influence of water molecules in the active site of human serum albumin (HSA) on its paclitaxel complex as well as their interaction is essential for clinical studies. Molecular docking of both crystal-HSA and solvated-HSA with paclitaxel was performed in the present work. The docking result shows that paclitaxel is inserted more deeply in the binding pocket of crystal-HSA than in the same site of solvated-HSA, and more intermolecular H-bonds are formed in the shrunken binding site of solvated-HSA...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26961385/rising-strengths-hong-kong-sar-in-bioinformatics
#15
REVIEW
Chiranjib Chakraborty, C George Priya Doss, Hailong Zhu, Govindasamy Agoramoorthy
Hong Kong's bioinformatics sector is attaining new heights in combination with its economic boom and the predominance of the working-age group in its population. Factors such as a knowledge-based and free-market economy have contributed towards a prominent position on the world map of bioinformatics. In this review, we have considered the educational measures, landmark research activities and the achievements of bioinformatics companies and the role of the Hong Kong government in the establishment of bioinformatics as strength...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26961384/insight-into-the-conformational-variations-in-soxyz-protein-complex-from-two-different-members-of-the-%C3%AE-proteobacterial-family-involved-in-sulfur-oxidation
#16
Sujay Ray, Angshuman Bagchi
Sulfur anions serve as the important environmental pollutants. Microbes use hydrogen sulfide in different redox reactions and thus make the environment pollution-free. The sulfur redox processes are performed by a gene cluster called the sox operon, possessed by a diverse set of microorganisms. However, most of the previous studies were confined to α-proteobacteria. In this work, we tried to elucidate the mechanistic details of sulfur oxidation in β-proteobacteria. We compared the molecular mechanism of sulfur oxidation process using Dechloromonas aromatica and Thiobacillus denitrificans...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26947220/identification-of-structurally-diverse-antimicrobials-through-sequential-application-of-pharmacophore-modeling-virtual-screening-molecular-docking-and-in-vitro-microbiological-assay
#17
Ruchi Mishra, Sarvesh Paliwal, Ankita Agarwal, Swapnil Sharma
Dihydrofolate reductase enzyme has been an attractive biological target for the design and development of antimicrobials. Considering this, we have attempted to identify novel dihydrofolate reductase inhibitors through our well-defined in silico and in vitro work flow. An accurate and predictive pharmacophore model comprising of one hydrogen bond acceptor, two hydrophobic and one ring aromatic was developed and utilized as a query to search the National Cancer Institute and Maybridge database leading to retrieval of various compounds which were filtered on the basis of estimated activity, fit value and Lipinski's violation...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26885647/prediction-of-phenotypic-effects-of-variants-observed-in-loc_os04g36720-of-fro1-gene-in-rice-oryza-sativa-l
#18
Rakesh Kumar Meena, Sayane Shome, Sanket Thakur
In rice, ferric-chelate reductase-1 (FRO1) (LOC_Os04g36720) gene was present on chromosome number 4 and its beginning and ending coordinates where coding sequence lies are 22182599 and 22186943, respectively. It plays a vital role in metal homeostasis and iron transportation in plants. Based on the alignment results, location of single-nucleotide variants is located in open reading frame and their effects of variants were predicted using SIFT sequence tool. The non-synonymous variants at position 342 and 436 lies in helical and coil parts of the protein, respectively, as predicted by Psi-pred server...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26879961/enhanced-prediction-and-characterization-of-cdk-inhibitors-using-optimal-class-distribution
#19
Abhigyan Nath, S Karthikeyan
Cyclin-dependent kinase inhibitors (CDKIs) govern the regulation of cyclin-dependent kinases, which are responsible for controlling cell cycle progression. The members of the CDKI protein family play important roles in many processes like tumor suppression, apoptosis, transcriptional regulation. The sequence similarity-based search methods to annotate putative CDKIs do not yield optimal performance due to sequence diversity of CDKIs. As a consequence, machine learning-based models have become viable choices for predicting CDKI...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/26857867/genome-wide-identification-and-comparative-analysis-of-copper-transporter-genes-in-plants
#20
Recep Vatansever, Ibrahim Ilker Ozyigit, Ertugrul Filiz
Copper (Cu) transporters have primary importance in maintenance of physiological limits of Cu homeostasis in plants. However, structural characterization of Cu transporters in many plant species is still limited. In this study, a total of 78 potential Cu transporter genes were identified from 18 different plant species. Study revealed that Cu transporters could be characterized with a CTR protein family (PF04145) domain, three putative transmembrane domains (TMDs), a single exon number, and a basic character...
June 2017: Interdisciplinary Sciences, Computational Life Sciences
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