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https://www.readbyqxmd.com/read/29349605/improved-effectiveness-of-stereotactic-radiosurgery-in-large-brain-metastases-by-individualized-isotoxic-dose-prescription-an-in-silico-study
#1
Jaap D Zindler, Jacqueline Schiffelers, Philippe Lambin, Aswin L Hoffmann
INTRODUCTION: In large brain metastases (BM) with a diameter of more than 2 cm there is an increased risk of radionecrosis (RN) with standard stereotactic radiosurgery (SRS) dose prescription, while the normal tissue constraint is exceeded. The tumor control probability (TCP) with a single dose of 15 Gy is only 42%. This in silico study tests the hypothesis that isotoxic dose prescription (IDP) can increase the therapeutic ratio (TCP/Risk of RN) of SRS in large BM. MATERIALS AND METHODS: A treatment-planning study with 8 perfectly spherical and 46 clinically realistic gross tumor volumes (GTV) was conducted...
January 18, 2018: Strahlentherapie und Onkologie: Organ der Deutschen Röntgengesellschaft ... [et Al]
https://www.readbyqxmd.com/read/29347843/combinatorial-design-and-virtual-screening-of-potent-anti-tubercular-fluoroquinolone-and-isothiazoloquinolone-compounds-utilizing-qsar-and-pharmacophore-modelling
#2
S Nandi, S Ahmed, A K Saxena
The virulence of tuberculosis infections resistant to conventional combination drug regimens cries for the design of potent fluoroquinolone compounds to be used as second line antimycobacterial chemotherapeutics. One of the most effective in silico methods is combinatorial design and high throughput screening by a ligand-based pharmacophore prior to experiment. The combinatorial design of a series of 3850 fluoroquinolone and isothiazoloquinolone compounds was then screened virtually by applying a topological descriptor based quantitative structure activity relationship (QSAR) for predicting highly active congeneric quinolone leads against Mycobacterium fortuitum and Mycobacterium smegmatis...
February 2018: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/29347108/in-silico-optimization-of-critical-currents-in-superconductors
#3
Gregory Kimmel, Ivan A Sadovskyy, Andreas Glatz
For many technological applications of superconductors the performance of a material is determined by the highest current it can carry losslessly-the critical current. In turn, the critical current can be controlled by adding nonsuperconducting defects in the superconductor matrix. Here we report on systematic comparison of different local and global optimization strategies to predict optimal structures of pinning centers leading to the highest possible critical currents. We demonstrate performance of these methods for a superconductor with randomly placed spherical, elliptical, and columnar defects...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346287/development-of-zika-virus-vaccines
#4
REVIEW
Huda Makhluf, Sujan Shresta
Zika virus (ZIKV) is a mosquito-borne flavivirus that emerged as a global threat following the most recent outbreak in Brazil in 2015. ZIKV infection of pregnant women is associated with fetal abnormalities such as microcephaly, and infection of adults can lead to Guillain-Barré syndrome, an autoimmune disease characterized by neurological deficits. Although there are currently licensed vaccines for other flaviviruses, there remains an urgent need for preventative vaccines against ZIKV infection. Herein we describe the current efforts to accelerate the development of ZIKV vaccines using various platforms, including live attenuated virus, inactivated virus, DNA and RNA, viral vectors, and in silico-predicted immunogenic viral epitopes...
January 18, 2018: Vaccines
https://www.readbyqxmd.com/read/29346071/identification-of-potential-inhibitors-against-nuclear-dam1-complex-subunit-ask1-of-candida-albicans-using-virtual-screening-and-md-simulations
#5
Himanshu Tripathi, Feroz Khan
Identification of hit compounds against specific target form the starting point for a drug discovery program. A consistent decline of new chemical entities (NCEs) in recent years prompted a challenge to explore newer approaches to discover potential hit compounds that in turn can be converted into leads, and ultimately drug with desired therapeutic efficacy. The vast amount of omics and activity data available in public databases offers an opportunity to identify novel targets and their potential inhibitors...
January 1, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29344244/identification-and-validation-of-psat1-as-a-potential-prognostic-factor-for-predicting-clinical-outcomes-in-patients-with-colorectal-carcinoma
#6
Cheng Qian, Yongsheng Xia, Yun Ren, Yan Yin, Anmei Deng
The aim of the present study was to explore the existence of known or candidate drug-target genes that are upregulated in colorectal cancer (CRC) and may serve as novel prognostic factors or therapeutic targets for this type of malignancy. An in silico analysis was conducted using the Oncomine tool to compare the expression levels of a list of drug-target genes between cancerous and normal tissues in 6 independent CRC cohorts retrieved from the Oncomine database. Phosphoserine aminotransferase 1 (PSAT1) was identified as the top-ranked upregulated gene in CRC tumors, and was highly expressed in patients with chemoresistant disease...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343815/microrna-145-5p-and-microrna-320a-encapsulated-in-endothelial-microparticles-contribute-to-the-progression-of-vasculitis-in-acute-kawasaki-disease
#7
Hideyuki Nakaoka, Keiichi Hirono, Seiji Yamamoto, Ichiro Takasaki, Kei Takahashi, Koshi Kinoshita, Asami Takasaki, Naonori Nishida, Mako Okabe, Wang Ce, Nariaki Miyao, Kazuyoshi Saito, Keijiro Ibuki, Sayaka Ozawa, Yuichi Adachi, Fukiko Ichida
Kawasaki Disease (KD) is an acute inflammatory disease that takes the form of systemic vasculitis. Endothelial microparticles (EMPs) have been recognized as an important transcellular delivery system. We hypothesized whether EMPs are involved in vasculitis in acute KD. Fifty patients with acute KD were enrolled, divided into two subgroups: those with coronary artery lesions (CAL) (n = 5) and those without CAL (NCAL) (n = 45). EMPs were measured using flow cytometry, and microRNA (miR) expression profiling was performed by microRNA array...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29341343/small-heat-shock-protein-b3-hspb3-mutation-in-an-axonal-charcot-marie-tooth-disease-family
#8
Da Eun Nam, Soo Hyun Nam, Ah Jin Lee, Young Bin Hong, Byung-Ok Choi, Ki Wha Chung
HSPB3 gene encodes a small heat-shock protein 27-like protein which has a high sequence homology with HSPB1. A mutation in the HSPB3 was reported as the putative underlying cause of distal hereditary motor neuropathy 2C (dHMN2C) in 2010. We identified a heterozygous mutation (c.352T>C, p.Tyr118His) in the HSPB3 from a Charcot-Marie-Tooth disease type 2 (CMT2) family by the method of targeted next generation sequencing. The mutation was located in the well conserved alpha-crystalline domain, and several in silico predictions indicated a pathogenic effect of the mutation...
January 17, 2018: Journal of the Peripheral Nervous System: JPNS
https://www.readbyqxmd.com/read/29340866/-in-silico-study-of-the-binding-of-two-novel-antagonists-to-the-nociceptin-receptor
#9
Stefano Della Longa, Alessandro Arcovito
Antagonists of the nociceptin receptor (NOP) are raising interest for their possible clinical use as antidepressant drugs. Recently, the structure of NOP in complex with some piperidine-based antagonists has been revealed by X-ray crystallography. In this study, a multi-flexible docking (MF-docking) procedure, i.e. docking to multiple receptor conformations extracted by preliminary molecular dynamics trajectories, together with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have been carried out to provide the binding mode of two novel NOP antagonists, one of them selective (BTRX-246040, formerly named LY-2940094) and one non selective (AT-076), i...
January 16, 2018: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29340790/an-automated-framework-for-qsar-model-building
#10
Samina Kausar, Andre O Falcao
BACKGROUND: In-silico quantitative structure-activity relationship (QSAR) models based tools are widely used to screen huge databases of compounds in order to determine the biological properties of chemical molecules based on their chemical structure. With the passage of time, the exponentially growing amount of synthesized and known chemicals data demands computationally efficient automated QSAR modeling tools, available to researchers that may lack extensive knowledge of machine learning modeling...
January 16, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29338812/comprehensive-assessment-of-the-quality-of-salmonella-whole-genome-sequence-data-available-in-public-sequence-databases-using-the-salmonella-in-silico-typing-resource-sistr
#11
James Robertson, Catherine Yoshida, Peter Kruczkiewicz, Celine Nadon, Anil Nichani, Eduardo N Taboada, John Howard Eagles Nash
Public health and food safety institutions around the world are adopting whole genome sequencing (WGS) to replace conventional methods for characterizing Salmonella for use in surveillance and outbreak response. Falling costs and increased throughput of WGS have resulted in an explosion of data, but questions remain as to the reliability and robustness of the data. Due to the critical importance of serovar information to public health, it is essential to have reliable serovar assignments available for all of the Salmonella records...
January 17, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29337192/combining-machine-learning-models-of-in-vitro-and-in-vivo-bioassays-improves-rat-carcinogenicity-prediction
#12
Davy Guan, Kevin Fan, Ian Spence, Slade Matthews
In vitro genotoxicity bioassays are cost-efficient methods of assessing potential carcinogens. However, many genotoxicity bioassays are inappropriate for detecting chemicals eliciting non-genotoxic mechanisms, such as tumour promotion, this necessitates the use of in vivo rodent carcinogenicity (IVRC) assays. In silico IVRC modelling could potentially address the low throughput and high cost of this assay. We aimed to develop and combine computational QSAR models of novel bioassays for the prediction of IVRC results and compare with existing software...
January 11, 2018: Regulatory Toxicology and Pharmacology: RTP
https://www.readbyqxmd.com/read/29337088/cross-regulatory-network-in-pseudomonas-aeruginosa-biofilm-genes-and-tio2-anatase-induced-molecular-perturbations-in-key-proteins-unraveled-by-a-systems-biology-approach
#13
Rani Anupama, S Sajitha Lulu, Amitava Mukherjee, Subramanian Babu
A systems biology approach was used to study all the biofilm related genes of P. aeruginosa PAO1, and the interaction of titanium dioxide (TiO2) anatase with biofilm related proteins. Among the 71 genes, the interactions of all the nodal pairs were extracted by STRING 10.5 database. The inter-relationship among these genes was predicted by constructing complete PPI network and visualized in Cytoscape v 3.4.0. Total number of nodes of the network was found to be 335 and edges were 795. The network was further investigated for its clusters and the best cluster was further analyzed for the hub proteins which significantly contribute in cross-regulation of the biofilm related process...
January 11, 2018: Gene
https://www.readbyqxmd.com/read/29336266/design-synthesis-evaluation-and-computational-studies-of-nipecotic-acid-acetonaphthone-hybrids-as-potential-antiepileptic-agents
#14
Ankit Seth, Piyoosh A Sharma, Avanish Tripathi, Priyanka K Choubey, Pavan Srivastava, Prabhash N Tripathi, Sushant Kumar Shrivastava
BACKGROUND: Nipecotic acid is considered to be one of the most potent inhibitors of neuronal and glial γ- aminobutyric acid (GABA) uptake in vitro. However nipecotic acid does not readily cross the blood-brain barrier (BBB) following peripheral administration, owing to its hydrophilic nature. OBJECTIVE: A series of substituted acetonaphthones tethered nipecotic acid derivatives were designed and synthesized with an aim to improve the lipophilicity and the blood-brain barrier (BBB) permeation...
January 15, 2018: Medicinal Chemistry
https://www.readbyqxmd.com/read/29336243/identification-of-in-vitro-red-fluorescent-protein-with-antipathogenic-activity-from-the-midgut-of-the-silkworm-bombyx-mori-l
#15
Manjunatha Ks Gowda, Anitha Peter, Mahantesha Bn Naika, P Niranjana, P Shamprasad
Biotic stress affects all organisms, including the silkworm (Bombyx mori L.) which also has a plethora of defense mechanisms against the infecting pathogens. The midgut plays an important role as a natural barrier and source of innate immunity. The present investigation was thus undertaken to identify an antiviral red fluorescent protein formed in the midgut of the silkworm Bombyx mori L. The digestive juice from fifth instar Kolar Gold silkworm larvae was collected and subjected to 40 % ammonium sulfate precipitation and purified by gel filtration chromatography (GFC)...
January 15, 2018: Protein and Peptide Letters
https://www.readbyqxmd.com/read/29332600/finding-novel-anti-carcinomas-compounds-by-targeting-sfrp4-through-molecular-modeling-docking-and-dynamic-simulation-studies
#16
M Hassan, M Azhar, Q Abbas, H Reza, A A Moustafa, S Shahzadi, Z Ashraf, S Y Seo
BACKGROUND: Secreted frizzled-related protein 4 (SFRP4) is a glycoprotein that act as a competitor of both canonical and non-canonical Wnt pathways. SFRP4 is mostly expressed in ovary and played a significant role as a target molecule to cure ovarian carcinoma. OBJECTIVE: Multiple chemical agonists are being used to cure ovary melanoma. We are interested to theoretically analyze the compounds through computational approaches for their inhibitory effects against SFRP4...
January 11, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29332594/in-vitro-and-in-silico-evaluation-of-non-quaternary-reactivators-of-ache-as-antidotes-of-organophosphorus-poisoning-a-new-hope-or-a-blind-alley
#17
Ondrej Soukup, Jan Korabecny, David Malinak, Eugenie Nepovimova, Ngoc Lam Pham, Kamil Musilek, Martina Hrabinova, Vendula Hepnarova, Rafael Dolezal, Petr Pavek, Petr Jost, Tereza Kobrlova, Jana Jankockova, Lukas Gorecki, Miroslav Psotka, Thuy Duong Nguyen, Karl Box, Breeze Outhwaite, Martina Ceckova, Ales Sofr, Daniel Jun, Kamil Kuca
BACKGROUND: In the last decade, the concept of uncharged reactivators potentially able to penetrate the CNS has been introduced as an alternative to the classic charged oxime reactivators. However, this concept brings with it several associated drawbacks such as higher lipophilicity, difficulty in administration, lower affinity to cholinesterases, and higher toxicity risk. OBJECTIVE: In this study we compare data obtained for a set of five classic charged reactivators and a set of three recently published uncharged oximes supplemented by two novel ones...
January 11, 2018: Medicinal Chemistry
https://www.readbyqxmd.com/read/29332373/use-of-adverse-outcome-pathways-aop-in-chemical-management-potential-advantages-and-limitations
#18
Jaeseong Jeong, Jinhee Choi
Amid revolutionary changes in toxicity assessment brought about by increasing regulation of chemicals, adverse outcome pathways (AOPs) have emerged as a useful framework to assess adverse effect of chemicals using molecular level effect, which aid in setting environmental regulation policies. AOPs are biological maps that describe mechanisms linking molecular initiating event to adverse outcomes at an individual level. Each AOP consists of a Molecular Initiating Event (MIE), Key Events (KEs), and an Adverse Outcome (AO)...
December 30, 2017: Environmental Health and Toxicology
https://www.readbyqxmd.com/read/29331223/structure-based-design-and-application-of-a-nucleotide-coenzyme-mimetic-ligand-application-to-the-affinity-purification-of-nucleotide-dependent-enzymes
#19
Marigianna Marinou, Dimitrios Platis, Farid S Ataya, Evangelia Chronopoulou, Dimitrios Vlachakis, Nikolaos E Labrou
In the present study, a structure-based approach was exploited for the in silico design of a nucleotide coenzyme mimetic ligand. The enzyme formate dehydrogenase (FDH) was employed as a model in our study. The biomimetic ligand was designed and synthesized based on a tryptamine/3-aminopropylphosphonic acid bi-substituted 1,3,5-triazine (Trz) scaffold (Tra-Trz-3APP), which potentially mimics the interactions of NAD+-FDH complex. Molecular docking studies of the biomimetic ligand predicted that it can occupy the same binding site as the natural coenzyme...
January 3, 2018: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29330771/inhibition-of-human%C3%A2-immunodeficiency-type-1-virus-hiv-1-life-cycle-by-different-egg-white-lysozymes
#20
Mandana Behbahani, Mokhtar Nosrati, Hassan Mohabatkar
Lysozyme is a relatively small enzyme with different biological activities, which is found in tears, saliva, egg white, and human milk. In the study, the anti-HIV-1 activity of lysozymes purified from quail, Meleagris, and hen egg white has been determined. For this end, a time-of-drug-addition assay was performed to identify the target of anti-HIV-1 agents and for determination of probable anti HIV-1 mechanism of the studied lysozyme, the binding affinity of the lysozymes to the human CD4 receptor was studied by molecular docking method...
January 13, 2018: Applied Biochemistry and Biotechnology
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