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https://www.readbyqxmd.com/read/28319747/integration-of-in-silico-methods-and-computational-systems-biology-to-explore-endocrine-disrupting-chemical-binding-with-nuclear-hormone-receptors
#1
P Ruiz, A Sack, M Wampole, S Bobst, M Vracko
Thousands of potential endocrine-disrupting chemicals present difficult regulatory challenges. Endocrine-disrupting chemicals can interfere with several nuclear hormone receptors associated with a variety of adverse health effects. The U.S. Environmental Protection Agency (U.S. EPA) has released its reviews of Tier 1 screening assay results for a set of pesticides in the Endocrine Disruptor Screening Program (EDSP), and recently, the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP) data...
March 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28317383/design-rules-for-enhanced-interfacial-shear-response-in-functionalized-carbon-fiber-epoxy-composites
#2
Baris Demir, Luke Christian Henderson, Tiffany R Walsh
Carbon-fiber reinforced composites are ideal light-weighting candidates to replace traditional engineering materials. The mechanical performance of these composites results from a complex interplay of influences operating over several length- and time-scales. The mechanical performance may therefore be limited by many factors, one of which being the modest interfacial adhesion between the carbon fiber and the polymer. Surface chemical modification of the fiber, via surface grafting of molecules, is one possible strategy to enhance interactions across the fiber-polymer interface...
March 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28317148/bortezomib-induced-peripheral-neuropathy-a-genome-wide-association-study-on-multiple-myeloma-patients
#3
Chiara Campo, Miguel Inacio da Silva Filho, Niels Weinhold, Seyed Hamidreza Mahmoudpour, Hartmut Goldschmidt, Kari Hemminki, Maximilian Merz, Asta Försti
The proteasome-inhibitor bortezomib was introduced into the treatment of multiple myeloma more than a decade ago. It is clinically beneficial, but peripheral neuropathy (PNP) is a side effect that may limit its use in some patients. To examine the possible genetic predisposing factors to PNP, we performed a genome-wide association study on 646 bortezomib-treated German multiple myeloma patients. Our aim was to identify genetic risk variants associated with the development of PNP as a serious side effect of the treatment...
March 20, 2017: Hematological Oncology
https://www.readbyqxmd.com/read/28316108/cry1a-b-16-toxin-from-bacillus-thuringiensis-theoretical-refinement-of-three-dimensional-structure-and-prediction-of-peptides-as-molecular-markers-for-detection-of-genetically-modified-organisms
#4
Alexandra Plácido, Andreia Coelho, Lucas Abreu do Nascimento, Andreanne Gomes Vasconcelos, Maria Fátima Barroso, Joilson Ramos-Jesus, Vladimir Costa, Francisco das Chagas Alves Lima, Cristina Delerue-Matos, Ricardo Martins Ramos, Mariela M Marani, José Roberto de Souza de Almeida Leite
Transgenic maize produced by the insertion of the Cry transgene into its genome became the second most cultivated crop worldwide. Cry gene from Bacillus thuringiensis kurstaki expresses protein derivatives of crystalline endotoxins which confer insect resistance onto the maize crop. Mandatory labeling of processed food containing or made by genetically modified organisms is in force in many countries, so, it is very urgent to develop fast and practical methods for GMO identification, e.g., biosensors. In the absence of an available empirical structure of Cry1A(b)16 protein, a theoretical model was effectively generated, in this work, by homology modeling and molecular dynamics simulations based on two available homologous protein structures...
March 18, 2017: Proteins
https://www.readbyqxmd.com/read/28315689/in-silico-prediction-of-hpxr-activators-using-structure-based-pharmacophore-modeling
#5
Nao Torimoto-Katori, Ruili Huang, Harutoshi Kato, Rikiya Ohashi, Menghang Xia
The activation of pregnane X receptor (PXR), a member of the nuclear receptor superfamily, can mediate potential drug-drug interactions by regulating the expression of several drug- mediated enzymes and transporters, resulting in reduced therapeutic efficacy or increased toxicity by producing reactive metabolites. Therefore, in the early stage of drug development, it is important to predict these risks using an in silico approach. We constructed a human PXR (hPXR) pharmacophore model based on known structural information of compounds that activate PXR...
March 15, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28315441/physico-chemical-characteristics-and-fibril-forming-capacity-of-carp-swim-bladder-collagens-and-exploration-of-their-potential-bioactive-peptides-by-in-silico-approaches
#6
Gaurav Kumar Pal, P V Suresh
This study explores the sustainable valorization of carp swim bladder by-products. The high-value molecule collagens were successfully extracted from carp swim bladder with a yield of∼60% (dry weight basis) and characterized by sodium dodecyl sulfate polyacrylamide gel electrophoresis, UV-spectrum and Fourier transform infrared spectroscopy. The extracted collagens showed the fibril-forming ability and high denaturation temperature (38-39°C). Furthermore, the extracted collagens subjected to preparing bioactive collagen hydrolysates with potential antioxidant activities...
March 14, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28315253/prediction-of-proteases-involved-in-peptide-generation
#7
Mercedes Arguello Casteleiro, Robert Stevens, Julie Klein
Clinical proteomics has led to the identification of a substantial number of disease-associated peptides and protein fragments in several conditions such as cancer, kidney, or cardiovascular diseases. In silico prediction tools that can facilitate linking of identified peptide biomarkers to predicted protease activity might therefore significantly contribute to the understanding of pathophysiological mechanisms of these diseases. Proteasix is an open-source, peptide-centric tool that can be used to predict in silico the proteases involved in naturally occurring peptide generation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315238/comprehensive-gas-phase-peptide-ion-structure-studies-using-ion-mobility-techniques-part-2-gas-phase-hydrogen-deuterium-exchange-for-ion-population-estimation
#8
Mahdiar Khakinejad, Samaneh Ghassabi Kondalaji, Amirmahdi Tafreshian, Stephen J Valentine
Gas-phase hydrogen/deuterium exchange (HDX) using D2O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data...
March 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28315223/t-cell-epitope-prediction
#9
George N Konstantinou
An epitope is a part of an immunogenic protein that can be recognized by the immune system. The peptides that can be recognized by the T-cell receptors after a particular antigen has been intracellularly processed, bound to at least one MHC molecule and expressed on the surface of the antigen presenting cell as a MHC-peptide complex, are called a T-cell epitope. Individuals who have at least one MHC molecule able to most avidly bind to allergenic amino acid sequences from an allergen, and at the same time have the appropriate T-cell clone that can recognize this MHC-peptide complex, are expected to be genetically prone to allergic reactions against that allergen...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28304311/frontotemporal-dementia-due-to-the-novel-grn-arg161glyfsx36-mutation
#10
Stefano Gazzina, Silvana Archetti, Antonella Alberici, Elisa Bonomi, Maura Cosseddu, Diego Di Lorenzo, Alessandro Padovani, Barbara Borroni
Progranulin is a multifunctional growth factor mainly expressed in neurons and microglia. Loss-of-function mutations in the Granulin (GRN) gene are causative of frontotemporal dementia with TAR DNA-binding protein-43 inclusions. We reported the case of a 51-year-old male patient affected by sporadic agrammatic variant of primary progressive aphasia, in whom we identified a novel heterozygous deletion in the exon 6 (g.10338_39delAG, p.Arg161GlyfsX36). Plasma progranulin levels were significantly reduced and in silico analysis predicted a premature termination codon...
March 18, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28303969/hbv-quasispecies-composition-in-lamivudine-failed-chronic-hepatitis-b-patients-and-its-influence-on-virological-response-to-tenofovir-based-rescue-therapy
#11
Priyanka Banerjee, Abhijit Chakraborty, Rajiv Kumar Mondal, Mousumi Khatun, Somenath Datta, Kausik Das, Pratap Pandit, Souvik Mukherjee, Soma Banerjee, Saurabh Ghosh, Saikat Chakrabarti, Abhijit Chowdhury, Simanti Datta
The present study sought to evaluate the structure of HBV quasispecies in Lamivudine (LMV)-failed chronic hepatitis B (CHB) patients and its impact in defining the subsequent virological responses to Tenofovir (TDF)-based rescue-therapy. By analyzing HBV clones encompassing reverse transcriptase (RT) and surface (S) region from LMV-failed and treatment-naïve CHB patients, we identified 5 classical and 12 novel substitutions in HBV/RT and 9 substitutions in immune-epitopes of HBV/S that were significantly associated with LMV failure...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28303229/cloning-and-characterization-of-squalene-synthase-and-cycloartenol-synthase-from-siraitia-grosvenorii
#12
Huan Zhao, Qi Tang, Changming Mo, Longhua Bai, Dongping Tu, Xiaojun Ma
Mogrosides and steroid saponins are tetracyclic triterpenoids found in Siraitia grosvenorii. Squalene synthase (SQS) and cycloartenol synthase (CAS) are key enzymes in triterpenoid and steroid biosynthesis. In this study, full-length cDNAs of SgSQS and SgCAS were cloned by a rapid amplification of cDNA-ends with polymerase chain reaction (RACE-PCR) approach. The SgSQS cDNA has a 1254 bp open reading frame (ORF) encoding 417 amino acids, and the SgCAS cDNA contains a 2298 bp ORF encoding 765 amino acids. Bioinformatic analysis showed that the deduced SgSQS protein has two transmembrane regions in the C-terminal...
March 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28303031/a-biologically-validated-hcv-e1e2-heterodimer-structural-model
#13
Matteo Castelli, Nicola Clementi, Jennifer Pfaff, Giuseppe A Sautto, Roberta A Diotti, Roberto Burioni, Benjamin J Doranz, Matteo Dal Peraro, Massimo Clementi, Nicasio Mancini
The design of vaccine strategies and the development of drugs targeting the early stages of Hepatitis C virus (HCV) infection are hampered by the lack of structural information about its surface glycoproteins E1 and E2, the two constituents of HCV entry machinery. Despite the recent crystal resolution of limited versions of both proteins in truncated form, a complete picture of the E1E2 complex is still missing. Here we combined deep computational analysis of E1E2 secondary, tertiary and quaternary structure with functional and immunological mutational analysis across E1E2 in order to propose an in silico model for the ectodomain of the E1E2 heterodimer...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302310/design-synthesis-and-anti-diabetic-activity-of-triazolotriazine-derivatives-as-dipeptidyl-peptidase-4-dpp-4-inhibitors
#14
Bhumika D Patel, Shraddha V Bhadada, Manjunath D Ghate
Type 2 diabetes mellitus (T2DM) is one of the major global metabolic disorders characterized by insulin resistance and chronic hyperglycemia. Inhibition of the enzyme, dipeptidyl peptidase-4 (DPP-4) has been proved as successful and safe therapy for the treatment of T2DM since last decade. In order to design novel DPP-4 inhibitors, various in silico studies such as 3D-QSAR, pharmacophore modeling and virtual screening were performed and on the basis of the combined results of them, total 50 triazolo[5,1-c][1,2,4]triazine derivatives were designed and mapped on the best pharmacophore model...
March 6, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28302029/in-silico-adme-studies-for-new-drug-discovery-from-chemical-compounds-to-chinese-herbal-medicines
#15
Guojun Yan, Xiaobing Wang, Zhou Chen, Xianhui Wu, Jinhuo Pan, Yushen Huang, Gang Wan, Zhaogang Yang
Nowadays, in-silico tools are widely used to provide the potential structure of the metabolites formed depending on the site of metabolism. These methods can also highlight the molecular moieties that help to direct the molecule into the cytochrome cavity so that the site of metabolism is in proximity to the catalytic center. In this mini-review, we summarized three aspects of the in-silico methods in the application of prediction the ADME (absorption, distribution, metabolism and excretion) properties of compounds: structure-based approaches for predicting molecular modeling of drug metabolizing enzymes; in-silico metabolite prediction; and pharmacophore models for analysis substrate specificity...
March 15, 2017: Current Drug Metabolism
https://www.readbyqxmd.com/read/28302028/quantum-mechanical-qm-calculations-applied-to-admet-drug-prediction-a-review
#16
Edeildo F Silva-Júnior, J X Araújo-Júnior, T M Aquino
The discovery of new drugs is generally considered a long and expensive process, which often leads to molecules with low efficacy and high toxicity, which in many cases can be related to metabolism. In an attempt to reduce these failures and the production costs of a new drug, in silico studies have been used to obtain important information about the behavior of these compounds in the metabolism phases: absorption, distribution, metabolism (or biotransformation) and elimination (or excretion). Quantum Mechanical (QM) calculations are based on Schrödinger's equation can be used to develop models and theoretical parameters able to explain properties observed experimentally...
March 15, 2017: Current Drug Metabolism
https://www.readbyqxmd.com/read/28302026/drug-metabolism-in-preclinical-drug-development-a-survey-of-the-discovery-process-toxicology-and-computational-tools
#17
Naiem T Issa, Henri Wathieu, Abiola Ojo, Stephen W Byers, Sivanesan Dakshanamurthy
Increased R & D spending and high failure rates exist in drug development, due in part to inadequate prediction of drug metabolism and its consequences in the human body. Hence, there is a need for computational methods to supplement and complement current biological assessment strategies. In this review, we provide an overview of drug metabolism in pharmacology, and discuss the current in vitro and in vivo strategies for assessing drug metabolism in preclinical drug development. We highlight computational tools available to the scientific community for the in silico prediction of drug metabolism, and examine how these tools have been implemented to produce drug-target signatures relevant to metabolic routes...
March 15, 2017: Current Drug Metabolism
https://www.readbyqxmd.com/read/28302016/validation-of-tzd-scaffold-as-potential-aris-pharmacophore-modelling-atom-based-3d-qsar-and-docking-studies
#18
Lalita Dahiya, Manoj Kumar Mahapatra, Ramandeep Kaur, Vipin Kumar, Manoj Kumar
Metabolic disorders associated with diabetic patients are a serious concern. Aldose reductase (ALR2) has been identified as first rate-limiting enzyme in the polyol pathway which catalyzes the reduction of glucose to sorbitol. It represents one of the validated targets to develop potential new chemical entities for the prevention and subsequent progression of microvascular diabetic complications. In order to further understand the intricate structural prerequisites of molecules to act as ALR2 inhibitors, ligand-based pharmacophore model, atom-based 3D-QSAR and structure based drug design studies have been performed on a series of 2,4-thiazolidinedione derivatives with ALR2 inhibitory activity...
March 15, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28300611/surface-area-volume-and-shape-descriptors-as-a-novel-tool-for-polymer-lead-design-and-discovery
#19
Jonatan Riis Christensen, Helena Meng-Lund, Holger Grohganz, Antti Poso, Tuomo Laitinen, Ossi Korhonen, Lene Jørgensen, Jari Pajander
In recent years, the demand and interest for functionalized polymers have increased for drug delivery purposes. Because of the increased interest, methods that can be used to predict physical and chemical properties of polymers prior to synthesis would be of high value for the design and development of novel polymer structures. Through use of molecular descriptors and Principal Component Analysis, this study explores the possibilities of using in silico methods for polymer design and characterization for property prediction...
March 12, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28300596/combined-virtual-screening-mmpbsa-molecular-docking-and-dynamics-studies-against-deadly-anthrax-an-in-silico-effort-to-inhibit-bacillus-anthracis-nucleoside-hydrolase
#20
Masoumeh Karami, Chiya Jalali, Sako Mirzaie
Anthrax is a deadly disease caused by Bacillus anthracis, a dangerous biological warfare agent employed for both military and terrorist purposes. A critical selective target for chemotherapy against this disease is nucleoside hydrolase (NH), an enzyme still not found in mammals. In the current study, we have performed molecular docking and dynamics studies, aiming to propose the new potent inhibitors of B. anthracis NH among National Cancer Institute (NCI) Diversity Set. We also analyzed the principal interactions of proposed compounds with the active site residues of NH and the relevant factors to biological activity...
March 12, 2017: Journal of Theoretical Biology
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