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https://www.readbyqxmd.com/read/27905517/g4ipdb-a-database-for-g-quadruplex-structure-forming-nucleic-acid-interacting-proteins
#1
Subodh Kumar Mishra, Arpita Tawani, Amit Mishra, Amit Kumar
Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ∆Tm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author's name and techniques that were used to detect their interactions...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27901142/an-optimized-charge-penetration-model-for-use-with-the-amoeba-force-field
#2
Joshua A Rackers, Qiantao Wang, Chengwen Liu, Jean-Philip Piquemal, Pengyu Ren, Jay W Ponder
The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27899966/analysis-of-the-molecular-mechanism-of-osteosarcoma-using-a-bioinformatics-approach
#3
Jianxun Yang, Ning Wang
The aim of this study was to explore the underlying molecular mechanism related to the process and progression of osteosarcoma (OS). The differentially expressed genes (DEGs) were downloaded from the Gene Expression Omnibus database. The pathway and gene ontology (GO) enrichment analysis, as well as transcription factor, tumor-associated gene and tumor suppressor gene analyses were performed to investigate the functions of DEGs. Next, the protein-protein interaction (PPI) network was constructed and module analysis was further assessed by cluster analysis with the overlapping neighborhood expansion (Cluster ONE) cytoscape plug-in...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899635/interpro-in-2017-beyond-protein-family-and-domain-annotations
#4
Robert D Finn, Teresa K Attwood, Patricia C Babbitt, Alex Bateman, Peer Bork, Alan J Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A Natale, Marco Necci, Gift Nuka, Christine A Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C Potter, Neil D Rawlings, Nicole Redaschi, Lorna Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger Sutton, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Ioannis Xenarios, Lai-Su Yeh, Siew-Yit Young, Alex L Mitchell
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899602/the-human-phenotype-ontology-in-2017
#5
Sebastian Köhler, Nicole A Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M Bello, Cornelius F Boerkoel, Kym M Boycott, Michael Brudno, Orion J Buske, Patrick F Chinnery, Valentina Cipriani, Laureen E Connell, Hugh J S Dawkins, Laura E DeMare, Andrew D Devereau, Bert B A de Vries, Helen V Firth, Kathleen Freson, Daniel Greene, Ada Hamosh, Ingo Helbig, Courtney Hum, Johanna A Jähn, Roger James, Roland Krause, Stanley J F Laulederkind, Hanns Lochmüller, Gholson J Lyon, Soichi Ogishima, Annie Olry, Willem H Ouwehand, Nikolas Pontikos, Ana Rath, Franz Schaefer, Richard H Scott, Michael Segal, Panagiotis I Sergouniotis, Richard Sever, Cynthia L Smith, Volker Straub, Rachel Thompson, Catherine Turner, Ernest Turro, Marijcke W M Veltman, Tom Vulliamy, Jing Yu, Julie von Ziegenweidt, Andreas Zankl, Stephan Züchner, Tomasz Zemojtel, Julius O B Jacobsen, Tudor Groza, Damian Smedley, Christopher J Mungall, Melissa Haendel, Peter N Robinson
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899562/the-chembl-database-in-2017
#6
Anna Gaulton, Anne Hersey, Michał Nowotka, A Patrícia Bento, Jon Chambers, David Mendez, Prudence Mutowo, Francis Atkinson, Louisa J Bellis, Elena Cibrián-Uhalte, Mark Davies, Nathan Dedman, Anneli Karlsson, María Paula Magariños, John P Overington, George Papadatos, Ines Smit, Andrew R Leach
ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 and 2014 Nucleic Acids Research Database Issues. Since then, alongside the continued extraction of data from the medicinal chemistry literature, new sources of bioactivity data have also been added to the database. These include: deposited data sets from neglected disease screening; crop protection data; drug metabolism and disposition data and bioactivity data from patents. A number of improvements and new features have also been incorporated...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899561/database-resources-of-the-national-center-for-biotechnology-information
#7
(no author information available yet)
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank(®) nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 37 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27855605/regulation-of-cell-cycle-associated-genes-by-transcription-factor-and-microrna
#8
Nitai Pada Bhattacharyya, Eashita Das, Sudha Bucha, Srijit Das, Ananyo Choudhury
BACKGROUND: Cell cycle is a complex process and regulated at transcriptional, post-transcriptional and post-translational levels. Large numbers of genes are implicated in the process. Abnormality in any stage of cell cycle may lead to diseases including cancer. OBJECTIVES AND METHODS: To gain global view of genes associated with cell cycle, their regulation by transcription factors and microRNAs, we collected genes related to cell cycle from different databases...
November 17, 2016: MicroRNA
https://www.readbyqxmd.com/read/27831898/a-characteristic-based-framework-for-multiple-sequence-aligners
#9
Alvaro Rubio-Largo, Leonardo Vanneschi, Mauro Castelli, Miguel A Vega-Rodriguez
The multiple sequence alignment is a well-known bioinformatics problem that consists in the alignment of three or more biological sequences (protein or nucleic acid). In the literature, a number of tools have been proposed for dealing with this biological sequence alignment problem, such as progressive methods, consistency-based methods, or iterative methods; among others. These aligners often use a default parameter configuration for all the input sequences to align. However, the default configuration is not always the best choice, the alignment accuracy of the tool may be highly boosted if specific parameter configurations are used, depending on the biological characteristics of the input sequences...
November 2, 2016: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/27822544/multiplexed-metagenomic-deep-sequencing-to-analyze-the-composition-of-high-priority-pathogen-reagents
#10
Michael R Wilson, Greg Fedewa, Mark D Stenglein, Judith Olejnik, Linda J Rennick, Sham Nambulli, Friederike Feldmann, W Paul Duprex, John H Connor, Elke Mühlberger, Joseph L DeRisi
Laboratories studying high-priority pathogens need comprehensive methods to confirm microbial species and strains while also detecting contamination. Metagenomic deep sequencing (MDS) inventories nucleic acids present in laboratory stocks, providing an unbiased assessment of pathogen identity, the extent of genomic variation, and the presence of contaminants. Double-stranded cDNA MDS libraries were constructed from RNA extracted from in vitro-passaged stocks of six viruses (La Crosse virus, Ebola virus, canine distemper virus, measles virus, human respiratory syncytial virus, and vesicular stomatitis virus)...
July 2016: MSystems
https://www.readbyqxmd.com/read/27812939/evaluating-functional-annotations-of-enzymes-using-the-gene-ontology
#11
Gemma L Holliday, Rebecca Davidson, Eyal Akiva, Patricia C Babbitt
The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of interest to predicting where misannotation has occurred to knowing how confident you can be in the annotations assigned to those proteins is critical. In this chapter we explore what makes an enzyme unique and how we can use GO to infer aspects of protein function based on sequence similarity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27794553/fuzdb-database-of-fuzzy-complexes-a-tool-to-develop-stochastic-structure-function-relationships-for-protein-complexes-and-higher-order-assemblies
#12
Marton Miskei, Csaba Antal, Monika Fuxreiter
FuzDB (http://protdyn-database.org) compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database have both (i) structural evidence demonstrating the structural multiplicity or dynamic disorder of the ID region(s) in the partner bound form of the protein and (ii) in vitro or in vivo biological evidence that indicates the significance of the fuzzy region(s) in the formation, function or regulation of the assembly...
October 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27789701/updates-in-rhea-an-expert-curated-resource-of-biochemical-reactions
#13
Anne Morgat, Thierry Lombardot, Kristian B Axelsen, Lucila Aimo, Anne Niknejad, Nevila Hyka-Nouspikel, Elisabeth Coudert, Monica Pozzato, Marco Pagni, Sébastien Moretti, Steven Rosanoff, Joseph Onwubiko, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan Bridge
Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant resource of expert-curated biochemical reactions designed for the functional annotation of enzymes and the description of metabolic networks. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions, using entities from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Here we describe developments in Rhea since our last report in the database issue of Nucleic Acids Research...
October 26, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27773681/topological-language-for-rna
#14
Fenix W D Huang, Christian M Reidys
: In this paper we introduce a novel, context-free grammar, RNAFeatures(*), capable of generating any RNA structure including pseudoknot structures (pk-structure). We represent pk-structures as orientable fatgraphs, which naturally leads to a filtration by their topological genus. Within this framework, RNA secondary structures correspond to pk-structures of genus zero. RNAFeatures(*) acts on formal, arc-labeled RNA secondary structures, called λ-structures. λ-structures correspond one-to-one to pk-structures together with some additional information...
December 2016: Mathematical Biosciences
https://www.readbyqxmd.com/read/27760124/rasbhari-optimizing-spaced-seeds-for-database-searching-read-mapping-and-alignment-free-sequence-comparison
#15
Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern
Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set...
October 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27604119/detection-and-molecular-identification-of-leishmania-rna-virus-lrv-in-iranian-leishmania-species
#16
Homa Hajjaran, Maryam Mahdi, Mehdi Mohebali, Katayoun Samimi-Rad, Angila Ataei-Pirkooh, Elham Kazemi-Rad, Saied Reza Naddaf, Reza Raoofian
Leishmania RNA virus (LRV) was first detected in members of the subgenus Leishmania (Viannia), and later, the virulence and metastasis of the New World species were attributed to this virus. The data on the presence of LRV in Old World species are confined to Leishmania major and a few Leishmania aethiopica isolates. The aim of this study was to survey the presence of LRV in various Iranian Leishmania species originating from patients and animal reservoir hosts. Genomic nucleic acids were extracted from 50 cultured isolates belonging to the species Leishmania major, Leishmania tropica, and Leishmania infantum...
December 2016: Archives of Virology
https://www.readbyqxmd.com/read/27601599/comprehensive-proteomic-analysis-of-human-milk-derived-extracellular-vesicles-unveils-a-novel-functional-proteome-distinct-from-other-milk-components
#17
Martijn J C van Herwijnen, Marijke I Zonneveld, Soenita Goerdayal, Esther N M Nolte-'t Hoen, Johan Garssen, Bernd Stahl, A F Maarten Altelaar, Frank A Redegeld, Marca H M Wauben
Breast milk contains several macromolecular components with distinctive functions, whereby milk fat globules and casein micelles mainly provide nutrition to the newborn, and whey contains molecules that can stimulate the newborn's developing immune system and gastrointestinal tract. Although extracellular vesicles (EV) have been identified in breast milk, their physiological function and composition has not been addressed in detail. EV are submicron sized vehicles released by cells for intercellular communication via selectively incorporated lipids, nucleic acids, and proteins...
November 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27590812/genomic-and-transcriptional-mapping-of-pamx41-archetype-of-a-new-lineage-of-bacteriophages-infecting-pseudomonas-aeruginosa
#18
Indira Cruz-Plancarte, Adrián Cazares, Gabriel Guarneros
: Previously, a collection of virulent phages infecting Pseudomonas aeruginosa were isolated from open water reservoirs and residual waters. Here, we described the comparative genomics of a set of five related phages from the collection, the physical structure of the genome, the structural proteomics of the virion and the transcriptional program of archetypal phage PaMx41. The phage genomes were closely associated with each other and with those of two other P. aeruginosa phages, 119X and PaP2, previously filed in the databases...
September 2, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27573064/oncogene-expression-modulation-in-cancer-cell-lines-by-dna-g-quadruplex-interactive-small-molecules
#19
Alexandra Paulo, Ana Paula Francisco
Nucleic acids are prone to structural polymorphism and a number of structures may be formed in addition to the well-known DNA double helix. Among these is a family of nucleic acid four-stranded structures known as G-quadruplexes (G4). These quadruplex structures can be formed by sequences containing repetitive guanine-rich tracks and the analysis of Non-B-DNA database indicated an enrichment of these sequences in genomic regions controlling cellular proliferation, such as for example in the promoter regions of c-MYC, k-RAS, c-KIT, HSP90 and VEGF among others...
August 29, 2016: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/27557553/development-of-a-multisystem-surveillance-database-for-transfusion-transmitted-infections-among-blood-donors-in-the-united-states
#20
Roger Y Dodd, Edward P Notari, Diane Nelson, Gregory A Foster, David E Krysztof, Zhanna Kaidarova, Lisa Milan-Benson, Debra A Kessler, Beth H Shaz, Farnaz Vahidnia, Brian Custer, Susan L Stramer
BACKGROUND: The frequency of positive test results for transfusion-transmitted infections (TTIs) among blood donors is an important index of safety; thus, appropriate monitoring is critical, particularly when there are changes in policies affecting donor suitability. STUDY DESIGN AND METHODS: Testing algorithms from three large blood systems were reviewed and consensus definitions for a surveillance-positive result for hepatitis B virus (HBV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), and human T-cell lymphotropic virus (HTLV) established...
August 25, 2016: Transfusion
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