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Structural bioinformatics

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https://www.readbyqxmd.com/read/28531277/genome-wide-discovery-of-viral-micrornas-based-on-phylogenetic-analysis-and-structural-evolution-of-various-human-papillomavirus-subtypes
#1
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission...
May 20, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28529482/mode-of-action-analyses-of-neferine-a-bisbenzylisoquinoline-alkaloid-of-lotus-nelumbo-nucifera-against-multidrug-resistant-tumor-cells
#2
Onat Kadioglu, Betty Y K Law, Simon W F Mok, Su-Wei Xu, Thomas Efferth, Vincent K W Wong
Neferine, a bisbenzylisoquinoline alkaloid isolated from the green seed embryos of Lotus (Nelumbo nucifera Gaertn), has been previously shown to have various anti-cancer effects. In the present study, we evaluated the effect of neferine in terms of P-glycoprotein (P-gp) inhibition via in vitro cytotoxicity assays, R123 uptake assays in drug-resistant cancer cells, in silico molecular docking analysis on human P-gp and in silico absorption, distribution, metabolism, and excretion (ADME), quantitative structure activity relationships (QSAR) and toxicity analyses...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28528876/modeling-covalent-modifier-drugs
#3
REVIEW
Ernest Awoonor-Williams, Andrew G Walsh, Christopher N Rowley
In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly...
May 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28526816/delineation-of-b-cell-epitopes-of-salmonella-enterica-serovar-typhi-hemolysin-e-potential-antibody-therapeutic-target
#4
Chai Fung Chin, Jing Yi Lai, Yee Siew Choong, Amy Amilda Anthony, Asma Ismail, Theam Soon Lim
Hemolysin E (HlyE) is an immunogenic novel pore-forming toxin involved in the pathogenesis of typhoid fever. Thus, mapping of B-cell epitopes of Salmonella enterica serovar Typhi (S. Typhi) is critical to identify key immunogenic regions of HlyE. A random 20-mer peptide library was used for biopanning with enriched anti-HlyE polyclonal antibodies from typhoid patient sera. Bioinformatic tools were used to refine, analyze and map the enriched peptide sequences against the protein to identify the epitopes. The analysis identified both linear and conformational epitopes on the HlyE protein...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526268/structural-and-functional-aspects-of-the-nonribosomal-peptide-synthetase-condensation-domain-superfamily-discovery-dissection-and-diversity
#5
REVIEW
Kristjan Bloudoff, T Martin Schmeing
Nonribosomal peptide synthetases (NRPSs) are incredible macromolecular machines that produce a wide range of biologically- and therapeutically-relevant molecules. During synthesis, peptide elongation is performed by the condensation (C) domain, as it catalyzes amide bond formation between the nascent peptide and the amino acid it adds to the chain. Since their discovery more than two decades ago, C domains have been subject to extensive biochemical, bioinformatic, mutagenic, and structural analyses. They are composed of two lobes each with homology to chloramphenicol acetyltransferase, have two binding sites for their two peptidyl carrier protein-bound ligands, and have an active site with conserved motif HHxxxDG located between the two lobes...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28525653/predicted-philogeny-secondary-conformational-structure-and-epitope-antigenicity-of-immunological-sequences-in-poultry
#6
L J Lara, A P Peconick, É J Fassani, A M P Júnior, P R B Chalfun, D L Raymundo, T A Barçante, J M de P Barçante
Poultry production is faced with different types of stresses that are responsible for issues of animal welfare as well as for economic losses. Moreover, the immunity decreases when animals are stressed. In silico analyses are important in reducing the cost and in increasing the accuracy of scientific results. A bioinformatics tool was used to perform ontology studies on 15 different immunological sequences of poultry. The mRNA structures and sequences with maximum antigenic residues were also predicted. No homology was found between the sequences of poultry and mammals...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28522994/new-potent-membrane-targeting-antibacterial-peptides-from-viral-capsid-proteins
#7
Susana A Dias, João M Freire, Clara Pérez-Peinado, Marco M Domingues, Diana Gaspar, Nuno Vale, Paula Gomes, David Andreu, Sónia T Henriques, Miguel A R B Castanho, Ana S Veiga
The increasing prevalence of multidrug-resistant bacteria urges the development of new antibacterial agents. With a broad spectrum activity, antimicrobial peptides have been considered potential antibacterial drug leads. Using bioinformatic tools we have previously shown that viral structural proteins are a rich source for new bioactive peptide sequences, namely antimicrobial and cell-penetrating peptides. Here, we test the efficacy and mechanism of action of the most promising peptides among those previously identified against both Gram-positive and Gram-negative bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28522832/the-fragment-hmga2-sh-3p20-from-hmga2-mrna-3-utr-promotes-the-growth-of-hepatoma-cells-by-upregulating-hmga2
#8
Yuan Wang, Fuquan Chen, Zhe Yang, Man Zhao, Shuqin Zhang, Yuen Gao, Jinyan Feng, Guang Yang, Weiying Zhang, Lihong Ye, Xiaodong Zhang
High mobility group A2 (HMGA2) plays a crucial role in the development of cancer. However, the mechanism by which HMGA2 promotes the growth of hepatocellular carcinoma (HCC) remains unclear. Here, we explore the hypothesis that HMGA2 may enhance the growth of hepatoma cells through a fragment based on the secondary structure of HMGA2 mRNA 3'-untranslated region (3'UTR). Bioinformatics analysis showed that HMGA2 mRNA displayed a hairpin structure within its 3'UTR, termed HMGA2-sh. Mechanistically, RNA immunoprecipitation assays showed that the microprocessor Drosha or DGCR8 interacted with HMGA2 mRNA in hepatoma cells...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28521678/ipgk-pseaac-identify-lysine-phosphoglycerylation-sites-in-proteins-by-incorporating-four-different-tiers-of-amino-acid-pairwise-coupling-information-into-the-general-pseaac
#9
Li-Ming Liu, Yan Xu, Kuo-Chen Chou
BACKGROUND: Occurring at Lys residues, the PGK (lysine phosphoglycerylation) is a special kind of post-translational modification (PTM). It may invert the charge potential of the modified residue and change the protein structures and functions, causing various diseases in liver, brain, and kidney. OBJECTIVE: From the angles of both basic research and drug development, we are facing a critical challenging problem: for an uncharacterized protein sequence containing many Lys residues, which ones can be of phosphoglycerylation, and which ones cannot? METHOD: To address this problem, we have developed a predictor called iPGK-PseAAC by incorporating into the general PseAAC (pseudo amino acid composition) with four different tiers of amino acid pairwise coupling information, where tiers 1, 2, 3, and 4 refer to the amino acid pairwise couplings between all the 1st, 2nd, 3rd, and 4th most contiguous residues along a protein segment, respectively...
May 15, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28520848/pattern-fusion-analysis-by-adaptive-alignment-of-multiple-heterogeneous-omics-data
#10
Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng, Juan Liu, Luonan Chen
Motivation: Integrating different omics profiles is a challenging task, which provides a comprehensive way to understand complex diseases in a multi-view manner. One key for such an integration is to extract intrinsic patterns in concordance with data structures, so as to discover consistent information across various data types even with noise pollution. Thus, we proposed a novel framework called "pattern fusion analysis" (PFA), which performs automated information alignment and bias correction, to fuse local sample-patterns (e...
May 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28512576/applications-of-contact-predictions-to-structural-biology
#11
REVIEW
Felix Simkovic, Sergey Ovchinnikov, David Baker, Daniel J Rigden
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28508547/functional-phosphatome-requirement-for-protein-homeostasis-networked-mitochondria-and-sarcomere-structure-in-c-%C3%A2-elegans-muscle
#12
Susann Lehmann, Joseph J Bass, Thomas F Barratt, Mohammed Z Ali, Nathaniel J Szewczyk
BACKGROUND: Skeletal muscle is central to locomotion and metabolic homeostasis. The laboratory worm Caenorhabditis elegans has been developed into a genomic model for assessing the genes and signals that regulate muscle development and protein degradation. Past work has identified a receptor tyrosine kinase signalling network that combinatorially controls autophagy, nerve signal to muscle to oppose proteasome-based degradation, and extracellular matrix-based signals that control calpain and caspase activation...
May 15, 2017: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/28508374/autodock-and-autodocktools-for-protein-ligand-docking-beta-site-amyloid-precursor-protein-cleaving-enzyme-1-bace1-as-a-case-study
#13
Nehme El-Hachem, Benjamin Haibe-Kains, Athar Khalil, Firas H Kobeissy, Georges Nemer
Computational docking and scoring techniques have revolutionized structural bioinformatics by providing unprecedented insights on key aspects of ligand-receptor interaction. Docking is used for optimizing known drugs and for identifying novel binders by predicting their binding mode and affinity. AutoDock and AutoDockTools are free of charge techniques that have been extensively cited in the literature as essential tools in structure-based drug design. Moreover, these methods are fast enough to permit virtual screening of ligand libraries containing tens of thousands of compounds...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28506204/antibiotic-effects-of-loperamide-homology-of-human-targets-of-loperamide-with-targets-in-acanthamoeba-spp
#14
Abdul Mannan Baig, Zohaib Rana, M Mohsin Mannan, S Sumayya Tariq, H R Ahmad
BACKGROUND: Loperamide is an anti-diarrheal drug prescribed for non-infectious diarrhea. The drug is an opioid receptor agonist, a blocker of voltage-dependent calcium channel (Cav) and a calmodulin (CaM) inhibitor on human cells. Loperamide has been reported to exert anti-amoebic effects against pathogenic strains of Acanthamoeba castellanii. OBJECTIVES: The precise mode of antibiotic action, cellular target homology with human counterparts and the pattern of cell death induced by loperamide in Acanthamoeba castellanii remain to be established...
April 25, 2017: Recent Patents on Anti-infective Drug Discovery
https://www.readbyqxmd.com/read/28505251/false-discovery-rate-control-incorporating-phylogenetic-tree-increases-detection-power-in-microbiome-wide-multiple-testing
#15
Jian Xiao, Hongyuan Cao, Jun Chen
Motivation: Next generation sequencing technologies have enabled the study of the human microbiome through direct sequencing of microbial DNA, resulting in an enormous amount of microbiome sequencing data. One unique characteristic of microbiome data is the phylogenetic tree that relates all the bacterial species. Closely related bacterial species have a tendency to exhibit a similar relationship with the environment or disease. Thus, incorporating the phylogenetic tree information can potentially improve the detection power for microbiome-wide association studies, where hundreds or thousands of tests are conducted simultaneously to identify bacterial species associated with a phenotype of interest...
May 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28505201/assessment-of-antibody-library-diversity-through-next-generation-sequencing-and-technical-error-compensation
#16
Marco Fantini, Luca Pandolfini, Simonetta Lisi, Michele Chirichella, Ivan Arisi, Marco Terrigno, Martina Goracci, Federico Cremisi, Antonino Cattaneo
Antibody libraries are important resources to derive antibodies to be used for a wide range of applications, from structural and functional studies to intracellular protein interference studies to developing new diagnostics and therapeutics. Whatever the goal, the key parameter for an antibody library is its complexity (also known as diversity), i.e. the number of distinct elements in the collection, which directly reflects the probability of finding in the library an antibody against a given antigen, of sufficiently high affinity...
2017: PloS One
https://www.readbyqxmd.com/read/28503665/probabilistic-modeling-of-bifurcations-in-single-cell-gene-expression-data-using-a-bayesian-mixture-of-factor-analyzers
#17
Kieran R Campbell, Christopher Yau
Modeling bifurcations in single-cell transcriptomics data has become an increasingly popular field of research. Several methods have been proposed to infer bifurcation structure from such data, but all rely on heuristic non-probabilistic inference. Here we propose the first generative, fully probabilistic model for such inference based on a Bayesian hierarchical mixture of factor analyzers. Our model exhibits competitive performance on large datasets despite implementing full Markov-Chain Monte Carlo sampling, and its unique hierarchical prior structure enables automatic determination of genes driving the bifurcation process...
March 15, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28502832/sexually-dimorphic-expression-in-developing-and-adult-gonads-shows-an-important-role-of-gonadal-soma-derived-factor-during-sex-differentiation-in-olive-flounder-paralichthys-olivaceus
#18
Yuezhong Liu, Wei Zhang, Xinxin Du, Jun Zhao, Xiaobing Liu, Xiaojing Li, Quanqi Zhang, Xubo Wang
Gonadal soma-derived factor (gsdf) is a new member of transforming growth factor beta (TGF-β) superfamily. As a teleost- and gonad-specific growth factor, gsdf has been indicated to play an important role in early germ cell development. However, little is known about its significance in germ cell development of olive flounder (Paralichthys olivaceus). In the present study, a 1338 bp gsdf gene was isolated from P. olivaceus for the first time. Bioinformatic analysis revealed that the genomic structure and synteny relationship of gsdf in teleosts were conserved...
May 11, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28502823/niaid-niehs-nhlbi-mcan-workshop-report-the-indoor-environment-and-childhood-asthma-implications-for-home-environmental-intervention-in-asthma-prevention-and-management
#19
Diane R Gold, Gary Adamkiewicz, Syed Hasan Arshad, Juan C Celedón, Martin D Chapman, Ginger L Chew, Donald N Cook, Adnan Custovic, Ulrike Gehring, James E Gern, Christine C Johnson, Suzanne Kennedy, Petros Koutrakis, Brian Leaderer, Herman Mitchell, Augusto A Litonjua, Geoffrey A Mueller, George T O'Connor, Dennis Ownby, Wanda Phipatanakul, Victoria Persky, Matthew S Perzanowski, Clare D Ramsey, Päivi M Salo, Julie M Schwaninger, Joanne E Sordillo, Avrum Spira, Shakira F Suglia, Alkis Togias, Darryl C Zeldin, Elizabeth C Matsui
Environmental exposures have been recognized as critical in the initiation and exacerbation of asthma, one of the most common chronic childhood diseases. The National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Environmental Health Sciences (NIEHS), National Heart, Lung, and Blood Institute (NHLBI), and Merck Childhood Asthma Network (MCAN) sponsored a joint workshop to discuss the current state of the science with respect to the indoor environment and its effects on the development and morbidity of childhood asthma...
May 10, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28502001/clustering-and-network-analysis-of-reverse-phase-protein-array-data
#20
Adam Byron
Molecular profiling of proteins and phosphoproteins using a reverse phase protein array (RPPA) platform, with a panel of target-specific antibodies, enables the parallel, quantitative proteomic analysis of many biological samples in a microarray format. Hence, RPPA analysis can generate a high volume of multidimensional data that must be effectively interrogated and interpreted. A range of computational techniques for data mining can be applied to detect and explore data structure and to form functional predictions from large datasets...
2017: Methods in Molecular Biology
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