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Library Discovery

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https://www.readbyqxmd.com/read/29149552/predicting-nano-bio-interactions-by-integrating-nanoparticle-libraries-and-quantitative-nanostructure-activity-relationship-modeling
#1
Wenyi Wang, Alexander Sedykh, Hainan Sun, Linlin Zhao, Daniel P Russo, Hongyu Zhou, Bing Yan, Hao Zhu
The discovery of biocompatible or bioactive nanoparticles for medicinal applications is an expensive and time-consuming process that may be significantly facilitated by incorporating more rational approaches combining both experimental and computational methods. However, it is currently hindered by two limitations: 1) the lack of high quality comprehensive data for computational modeling, and 2) the lack of an effective modeling method for the complex nanomaterial structures. In this study, we tackled both issues by first synthesizing a large library of nanoparticles and obtained comprehensive data on their characterizations and bioactivities...
November 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/29147535/a-platform-for-high-throughput-screening-of-dna-encoded-catalyst-libraries-in-organic-solvents
#2
K Delaney Hook, John T Chambers, Ryan Hili
We have developed a novel high-throughput screening platform for the discovery of small-molecules catalysts for bond-forming reactions. The method employs an in vitro selection for bond-formation using amphiphilic DNA-encoded small molecules charged with reaction substrate, which enables selections to be conducted in a variety of organic or aqueous solvents. Using the amine-catalysed aldol reaction as a catalytic model and high-throughput DNA sequencing as a selection read-out, we demonstrate the 1200-fold enrichment of a known aldol catalyst from a library of 16...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29144001/biological-evaluation-and-energetic-analyses-of-novel-gsk-3%C3%AE-inhibitors
#3
Denan Zhang, Lei Liu, Lin Pang, Qing Jin, Kehui Ke, Ming Hu, Jingbo Yang, Weifang Ma, Hongbo Xie, Xiujie Chen
Glycogen synthase kinase-3 beta (GSK-3β) is involved in multiple signaling pathways. Consistent with its critical roles in normal cells, abnormalities in GSK-3β activity have been implicated in diabetes, heart disease, Parkinson disease and Alzheimer's disease. In this study, a series of new scaffolds of small molecule inhibitors of GSK-3β were identified by virtual screening and bioassay. Candidates that adhere to drug-like criteria from a virtual library of compounds were tested using computational docking studies...
November 16, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29143774/disrupting-vegf-vegfr1-interaction-de-novo-designed-linear-helical-peptides-to-mimic-the-vegf13-25-fragment
#4
Beatriz Balsera, M Ángeles Bonache, Marie Reille-Seroussi, Nathalie Gagey-Eilstein, Michel Vidal, Rosario González-Muñiz, María Jesús Pérez de Vega
The interaction between vascular endothelial growth factor (VEGF) and its receptors (VEGFR) has important implications in angiogenesis and cancer, which moved us to search for peptide derivatives able to block this protein-protein interaction. In a previous work we had described a collection of linear 13-mer peptides specially designed to adopt helical conformations (Ac-SSEEX⁵ARNX⁸AAX(12)N-NH₂), as well as the evaluation of seven library components for the inhibition of the interaction of VEGF with its Receptor 1 (VEGFR1)...
October 28, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29139094/investigating-the-therapeutic-potential-and-mechanism-of-curcumin-in-breast-cancer-based-on-rna-sequencing-and-bioinformatics-analysis
#5
Rong Wang, Jinbin Li, Yulan Zhao, Yapeng Li, Ling Yin
BACKGROUND: Breast cancer is a prevalent cancer in female. This study aims to investigate the therapeutic potential and mechanism of curcumin in breast cancer. METHODS: After cultivation, human breast cancer cells (MCF-7 cells) were treated with 0.1% (v/v) 15 µmol/ml curcumin-dimethylsulfoxide solution and 0.1% (v/v) dimethylsulfoxide, respectively, at 37 °C and 5% CO2 for 48 h. Total RNA was extracted, cDNA library was constructed, and cDNAs were amplified and sequenced...
November 14, 2017: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/29137138/metabolic-profile-of-the-cellulolytic-industrial-actinomycete-thermobifida-fusca
#6
Niti Vanee, J Paul Brooks, Stephen S Fong
Actinomycetes have a long history of being the source of numerous valuable natural products and medicinals. To expedite product discovery and optimization of biochemical production, high-throughput technologies can now be used to screen the library of compounds present (or produced) at a given time in an organism. This not only facilitates chemical product screening, but also provides a comprehensive methodology to the study cellular metabolic networks to inform cellular engineering. Here, we present some of the first metabolomic data of the industrial cellulolytic actinomycete Thermobifida fusca generated using LC-MS/MS...
November 11, 2017: Metabolites
https://www.readbyqxmd.com/read/29136547/natural-products-used-as-a-chemical-library-for-protein-protein-interaction-targeted-drug-discovery
#7
Xuemei Jin, Kyungro Lee, Nam Hee Kim, Hyun Sil Kim, Jong In Yook, Jiwon Choi, Kyoung Tai No
Protein-protein interactions (PPIs), which are essential for cellular processes, have been recognized as attractive therapeutic targets. Therefore, the construction of a PPI-focused chemical library is an inevitable necessity for future drug discovery. Natural products have been used as traditional medicines to treat human diseases for millennia; in addition, their molecular scaffolds have been used in diverse approved drugs and drug candidates. The recent discovery of the ability of natural products to inhibit PPIs led us to use natural products as a chemical library for PPI-targeted drug discovery...
October 27, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29133809/stromatolites-on-the-rise-in-peat-bound-karstic-wetlands
#8
Bernadette C Proemse, Rolan S Eberhard, Chris Sharples, John P Bowman, Karen Richards, Michael Comfort, Leon A Barmuta
Stromatolites are the oldest evidence for life on Earth, but modern living examples are rare and predominantly occur in shallow marine or (hyper-) saline lacustrine environments, subject to exotic physico-chemical conditions. Here we report the discovery of living freshwater stromatolites in cool-temperate karstic wetlands in the Giblin River catchment of the UNESCO-listed Tasmanian Wilderness World Heritage Area, Australia. These stromatolites colonize the slopes of karstic spring mounds which create mildly alkaline (pH of 7...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133785/significance-estimation-for-large-scale-metabolomics-annotations-by-spectral-matching
#9
Kerstin Scheubert, Franziska Hufsky, Daniel Petras, Mingxun Wang, Louis-Félix Nothias, Kai Dührkop, Nuno Bandeira, Pieter C Dorrestein, Sebastian Böcker
The annotation of small molecules in untargeted mass spectrometry relies on the matching of fragment spectra to reference library spectra. While various spectrum-spectrum match scores exist, the field lacks statistical methods for estimating the false discovery rates (FDR) of these annotations. We present empirical Bayes and target-decoy based methods to estimate the false discovery rate (FDR) for 70 public metabolomics data sets. We show that the spectral matching settings need to be adjusted for each project...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29132906/a-selective-knockout-method-for-discovery-of-minor-active-components-from-plant-extracts-feasibility-and-challenges-as-illustrated-by-an-application-to-salvia-miltiorrhiza
#10
Xue-Yan Li, Hong-Jin Tang, Liu Zhang, Lin Yang, Ping Li, Jun Chen
Natural products have been recognized to play an invaluable role in drug discovery. However, efficient discovery of minor active constituents from natural sources is challenging due to the low abundance and complex matrices. In this study, we developed a selective knockout method to discover minor bioactive components from complex phytochemical mixtures, using a Chinese medicine as an example. Based on the chromatographic fingerprint, six major components in the ethyl acetate extract of the root of Salvia miltiorrhiza (EASM) were selectively knocked out via high-resolution peak fraction (HRPF) approach...
October 7, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29132314/proteomics-in-non-human-primates-utilizing-rna-seq-data-to-improve-protein-identification-by-mass-spectrometry-in-vervet-monkeys
#11
J Michael Proffitt, Jeremy Glenn, Anthony J Cesnik, Avinash Jadhav, Michael R Shortreed, Lloyd M Smith, Kylie Kavanagh, Laura A Cox, Michael Olivier
BACKGROUND: Shotgun proteomics utilizes a database search strategy to compare detected mass spectra to a library of theoretical spectra derived from reference genome information. As such, the robustness of proteomics results is contingent upon the completeness and accuracy of the gene annotation in the reference genome. For animal models of disease where genomic annotation is incomplete, such as non-human primates, proteogenomic methods can improve the detection of proteins by incorporating transcriptional data from RNA-Seq to improve proteomics search databases used for peptide spectral matching...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29130157/target-discovery-for-precision-medicine-using-high-throughput-genome-engineering
#12
Xinyi Guo, Poonam Chitale, Neville E Sanjana
Over the past few years, programmable RNA-guided nucleases such as the CRISPR/Cas9 system have ushered in a new era of precision genome editing in diverse model systems and in human cells. Functional screens using large libraries of RNA guides can interrogate a large hypothesis space to pinpoint particular genes and genetic elements involved in fundamental biological processes and disease-relevant phenotypes. Here, we review recent high-throughput CRISPR screens (e.g. loss-of-function, gain-of-function, and targeting noncoding elements) and highlight their potential for uncovering novel therapeutic targets, such as those involved in cancer resistance to small molecular drugs and immunotherapies, tumor evolution, infectious disease, inborn genetic disorders, and other therapeutic challenges...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29126180/replong-de-novo-repeat-identification-using-long-read-sequencing-data
#13
Rui Guo, Yan-Ran Li, Shan He, Le Ou-Yang, Yiwen Sun, Zexuan Zhu
Motivation: The identification of repetitive elements is important in genome assembly and phylogenetic analyses. The existing de novo repeat identification methods exploiting the use of short reads are impotent in identifying long repeats. Since long reads are more likely to cover repeat regions completely, using long reads is more favorable for recognizing long repeats. Summary: In this study, we propose a novel de novo repeat elements identification method namely RepLong based on PacBio long reads...
November 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29124927/integrated-continuous-emulsion-creamer
#14
Wesley Cochrane, Amber L Hackler, Valerie J Cavett, Alexander K Price, Brian M Paegel
Reaction incubation is ubiquitous in high-throughput screening workflows, including those at the microfluidic droplet scale. Fully integrated microfluidic processors that generate, incubate, and sort droplets for continuous droplet screening must passively handle a flowing emulsion such that droplet-droplet incubation time variation is minimized. Here, we disclose an integrated microfluidic emulsion creamer that close packs assay droplets by draining away excess oil through microfabricated drain channels. The drained oil co-flows with creamed emulsion and then reintroduces the oil to disperse the droplets at the circuit terminus for analysis...
November 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29123330/markov-logic-networks-for-adverse-drug-event-extraction-from-text
#15
Sriraam Natarajan, Vishal Bangera, Tushar Khot, Jose Picado, Anurag Wazalwar, Vitor Santos Costa, David Page, Michael Caldwell
Adverse drug events (ADEs) are a major concern and point of emphasis for the medical profession, government, and society. A diverse set of techniques from epidemiology, statistics, and computer science are being proposed and studied for ADE discovery from observational health data (e.g., EHR and claims data), social network data (e.g., Google and Twitter posts), and other information sources. Methodologies are needed for evaluating, quantitatively measuring, and comparing the ability of these various approaches to accurately discover ADEs...
May 2017: Knowledge and Information Systems
https://www.readbyqxmd.com/read/29122440/exploiting-the-human-peptidome-for-novel-antimicrobial-and-anticancer-agents
#16
Matteo Bosso, Ludger Ständker, Frank Kirchhoff, Jan Münch
Infectious diseases and cancers are leading causes of death and pose major challenges to public health. The human peptidome encompasses millions of compounds that display an enormous structural and functional diversity and represents an excellent source for the discovery of endogenous agents with antimicrobial and/or anticancer activity. Here, we discuss how to exploit the human peptidome for novel antimicrobial and anticancer agents through the generation of peptide libraries from human body fluids and tissues and stepwise purification of bioactive compounds...
October 31, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29122012/drug-target-ontology-to-classify-and-integrate-drug-discovery-data
#17
Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, Tudor I Oprea, Stephan C Schürer
BACKGROUND: One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome...
November 9, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/29120164/process-function-data-mining-for-the-discovery-of-solid-state-iron-oxide-pv
#18
Elana Borvick, Assaf Y Anderson, Hannah-Noa Barad, Maayan Priel, David A Keller, Adam Ginsburg, Kevin J Rietwyk, Simcha Meir, Arie Zaban
Data mining tools have been known to be useful for analyzing large material data sets generated by high-throughput methods. Typically, the descriptors used for the analysis are structural descriptors, which can be difficult to obtain and to tune according to the results of the analysis. In this Research Article, we show the use of deposition process parameters as descriptors for analysis of a photovoltaics data set. To create a data set, solar cell libraries were fabricated using iron oxide as the absorber layer deposited using different deposition parameters, and the photovoltaic performance was measured...
November 9, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/29116686/protocols-for-the-design-of-kinase-focused-compound-libraries
#19
Edgar Jacoby, Berthold Wroblowski, Christophe Buyck, Jean-Marc Neefs, Christophe Meyer, Maxwell D Cummings, Herman van Vlijmen
Protocols for the design of kinase-focused compound libraries are presented. Kinase-focused compound libraries can be differentiated based on the design goal. Depending on whether the library should be a discovery library specific for one particular kinase, a general discovery library for multiple distinct kinase projects, or even phenotypic screening, there exists today a variety of in silico methods to design candidate compound libraries. We address the following scenarios: 1) Datamining of SAR databases and kinase focused vendor catalogues; 2) Predictions and virtual screening; 3) Structure-based design of combinatorial kinase inhibitors; 4) Design of covalent kinase inhibitors; 5) Design of macrocyclic kinase inhibitors; and 6) Design of allosteric kinase inhibitors and activators...
November 8, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/29116522/monitoring-phage-biopanning-by-next-generation-sequencing
#20
Anna Vaisman-Mentesh, Yariv Wine
Phage display has enabled the rapid isolation of antigen-specific antibodies from combinatorial libraries of the variable heavy chain gene (VH) and variable light chain gene (VL). The method is based on genetic engineering of bacteriophages and repeated rounds of antigen-guided selection by phage biopanning.Next-Generation Sequencing (NGS) coupled with bioinformatics are powerful tools for analyzing the large number of DNA sequences present in an immune library.Here, we describe a method that demonstrates how NGS analysis enhances phage biopanning of complex antibody libraries as well as facilitates the antibody discovery process...
2018: Methods in Molecular Biology
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