keyword
MENU ▼
Read by QxMD icon Read
search

in silico prediction

keyword
https://www.readbyqxmd.com/read/28926980/indexing-natural-products-for-their-potential-anti-diabetic-activity-filtering-and-mapping-discriminative-physicochemical-properties
#1
Mouhammad Zeidan, Mahmoud Rayan, Nuha Zeidan, Mizied Falah, Anwar Rayan
Diabetes mellitus (DM) poses a major health problem, for which there is an unmet need to develop novel drugs. The application of in silico techniques and optimization algorithms is instrumental to achieving this goal. A set of 97 approved anti-diabetic drugs, representing the active domain, and a set of 2892 natural products, representing the inactive domain, were used to construct predictive models and to index anti-diabetic bioactivity. Our recently-developed approach of 'iterative stochastic elimination' was utilized...
September 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28926139/the-synonymous-nucleotide-substitution-rhd-1056c-g-alters-mrna-splicing-associated-with-serologically-weak-d-phenotype
#2
Sejong Chun, Jae Won Yun, Geon Park, Duck Cho
BACKGROUND: D antigen is one of the most clinically significant blood group antigens. Variation of the RHD gene can cause weak D or partial D phenotypes. While most variations are missense substitutions with amino acid changes, those without are called "silent" or "synonymous" substitutions. Synonymous substitutions often have little effect on the protein, not altering the phenotype. However, effect on splicing can affect end-product protein. We report a new synonymous variation, RHD 1056C>G, that resulted in weak D phenotype, and predicted its effect with various in silico methods...
September 19, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28924942/exploring-the-anti-proliferative-activity-of-pelargonium-sidoides-dc-with-in-silico-target-identification-and-network-pharmacology
#3
A S P Pereira, M J Bester, Z Apostolides
Pelargonium sidoides DC (Geraniaceae) is a medicinal plant indigenous to Southern Africa that has been widely evaluated for its use in the treatment of upper respiratory tract infections. In recent studies, the anti-proliferative potential of P. sidoides was shown, and several phenolic compounds were identified as the bioactive compounds. Little, however, is known regarding their anti-proliferative protein targets. In this study, the anti-proliferative mechanisms of P. sidoides through in silico target identification and network pharmacology methodologies were evaluated...
September 18, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28924046/in-silico-modeling-of-the-cryptic-e2-ubiquitin-binding-site-of-e6-associated-protein-e6ap-ube3a-reveals-the-mechanism-of-polyubiquitin-chain-assembly
#4
Virginia P Ronchi, Elizabeth D Kim, Christopher M Summa, Jennifer M Klein, Arthur L Haas
To understand the mechanism for assembly of Lys(48)-linked polyubiquitin degradation signals, we previously demonstrated the E6AP/UBE3A ligase harbors two functionally-distinct E2~ubiquitin binding sites: a high-affinity Site 1 required for E6AP Cys(820)~ubiquitin thioester formation and a canonical Site 2 responsible for subsequent chain elongation. Ordered binding to Sites 1 and 2 is here revealed by observation of UbcH7~ubiquitin-dependent substrate inhibition of chain formation at micromolar concentrations...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28924017/in-silico-analysis-of-the-regulation-of-the-photosynthetic-electron-transport-chain-in-c3-plants
#5
Alejandro Morales, Xinyou Yin, Jeremy Harbinson, Steven Michiel Driever, Jaap Molenaar, David M Kramer, Paul Struik
We present a new simulation model of the reactions in the photosynthetic electron transport chain of C3 species. We show that including recent insights about the regulation of the thylakoid proton motive force, ATP/NADPH balancing mechanisms (cyclic and non-cyclic alternative electron transport), and regulation of Rubisco activity, leads to emergent behaviors that may affect the operation and regulation of photosynthesis under different dynamic environmental conditions. The model was parameterized with experimental results in the literature, with a focus on Arabidopsis thaliana...
September 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28923030/the-eef1a2-gene-expression-as-risk-predictor-in-localized-prostate-cancer
#6
Thomas Stefan Worst, Frank Waldbillig, Abdallah Abdelhadi, Cleo-Aron Weis, Maria Gottschalt, Annette Steidler, Jost von Hardenberg, Maurice Stephan Michel, Philipp Erben
BACKGROUND: Besides clinical stage and Gleason score, risk-stratification of prostate cancer in the pretherapeutic setting mainly relies on the serum PSA level. Yet, this is associated with many uncertainties. With regard to therapy decision-making, additional markers are needed to allow an exact risk prediction. Eukaryotic translation elongation factor 1 alpha 2 (EEF1A2) was previously suggested as driver of tumor progression and potential biomarker. In the present study its functional and prognostic relevance in prostate cancer was investigated...
September 18, 2017: BMC Urology
https://www.readbyqxmd.com/read/28922667/integrated-strategy-for-mutagenicity-prediction-applied-to-food-contact-chemicals
#7
Serena Manganelli, Benoît Schilter, Emilio Benfenati, Alberto Manganaro, Elena Lo Piparo
Food contamination due to unintentional leakage of chemicals from food contact materials (FCM) is a source of increasing concern. Since for many of these substances, only limited or no toxicological data are available, the development of alternative methodologies to establish rapidly and cost-efficiently level of safety concern is critical to ensure adequate consumer protection. Computational toxicology methods are considered the most promising solutions to cope with this data gap. In particular, mutagenicity assessment has a particular relevance and is a mandatory requirement for all substances released from plastic FCM, regardless how low migration and exposure are...
September 18, 2017: ALTEX
https://www.readbyqxmd.com/read/28921840/the-role-of-cadherin-genes-in-five-major-psychiatric-disorders-a-literature-update
#8
REVIEW
Ziarih Hawi, Janette Tong, Callum Dark, Hannah Yates, Beth Johnson, Mark A Bellgrove
Converging evidence from candidate gene, genome-wide linkage, and association studies support a role of cadherins in the pathophysiology of five major psychiatric disorders including attention deficit hyperactivity disorder, autism spectrum disorder (ASD), schizophrenia (SCZ), bipolar disorder (BD), and major depressive disorder (MDD). These molecules are transmembrane proteins which act as cell adhesives by forming adherens junctions (AJs) to bind cells within tissues. Members of the cadherin superfamily are also involved in biological processes such as signal transduction and plasticity that have been implicated in the etiology of major psychiatric conditions...
September 18, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28921536/technical-note-a-simulation-study-on-the-feasibility-of-radiotherapy-dose-enhancement-with-calcium-tungstate-and-hafnium-oxide-nano-and-microparticles
#9
Nicholas J Sherck, You-Yeon Won
PURPOSE: To assess the radiotherapy dose enhancement (RDE) potential of calcium tungstate (CaWO4 ) and hafnium oxide (HfO2 ) nano- and microparticles (NPs). A Monte Carlo simulation study was conducted to gauge their respective RDE potentials relative to that of the broadly studied gold (Au) NP. The study was warranted due to the promising clinical and preclinical studies involving both CaWO4 and HfO2 NPs as RDE agents in the treatment of various types of cancers. The study provides a baseline RDE to which future experimental RDE trends can be compared to...
September 18, 2017: Medical Physics
https://www.readbyqxmd.com/read/28920551/a-comprehensive-in-silico-analysis-of-huntingtin-and-its-interactome
#10
Valentina Brandi, Valentina Di Lella, Maria Marino, Paolo Ascenzi, Fabio Polticelli
A polyglutamine expansion of the N-terminal region of huntingtin (Htt) causes Huntington's disease (HD), a severe neurodegenerative disorder. Htt huge multidomain structure, the presence of disordered regions, and the lack of sequence homologs of known structure, so far prevented structural studies of Htt, making the study of its structure-function relationships very difficult. In this work, the presence and location of five Htt ordered domains (named from Hunt1 to Hunt5) has been detected and the structure of these domains has been predicted for the first time using a combined threading/ab initio modelling approach...
September 18, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28919695/%C3%AE-defensins-an-innate-defense-for-bovine-mastitis
#11
REVIEW
Ankita Gurao, Sudhir Kumar Kashyap, Ravinder Singh
Immune challenges are inevitable for livestock that are exposed to a varied range of adverse conditions ranging from environmental to pathogenic stresses. The β-defensins are antimicrobial peptides, belonging to "defensin" family and therefore acts as the first line of defense against the major infections occurring in dairy cattle including intramammary infections. The better resistance to mastitis displayed by Bos indicus is implicit in the fact that they have better adapted and also has more sequence variation with rare allele conserved due to lesser artificial selection pressure than that of Bos taurus...
August 2017: Veterinary World
https://www.readbyqxmd.com/read/28919218/cardiologist-s-point-of-view-novel-ecg-biomarkers-and-in-silico-models-for-proarrhythmic-risk-prediction-are-we-ready
#12
Jay W Mason
The CiPA initiative is well underway, but in its early stages. Are we ready for it? There are several issues that bear on the success of this multidisciplinary effort related to (1) the final testing paradigm that will result, (2) the way in which discrepancies in test methods will be handled, (3) commercialization of the testing methods, (4) quantitative understanding of arrhythmia risk of the 6 non-hERG channels being tested, (5) validity of the CiPA drug list, and (6) ultimate clinical validation.
August 15, 2017: Journal of Electrocardiology
https://www.readbyqxmd.com/read/28918320/in-silico-interaction-analysis-of-cannabinoid-receptor-interacting-protein-1b-crip1b-cb1-cannabinoid-receptor
#13
Pratishtha Singh, Anjali Ganjiwale, Allyn C Howlett, Sudha M Cowsik
Cannabinoid Receptor Interacting Protein isoform 1b (CRIP1b) is known to interact with the CB1 receptor. Alternative splicing of the CNRIP1 gene produces CRIP1a and CRIP1b with a difference in the third exon only. Exons 1 and 2 encode for a functional domain in both proteins. CRIP1a is involved in regulating CB1 receptor internalization, but the function of CRIP1b is not very well characterized. Since there are significant identities in functional domains of these proteins, CRIP1b is a potential target for drug discovery...
September 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28918038/strategies-for-in%C3%A2-vivo-screening-and-mitigation-of-hepatotoxicity-associated-with-antisense-drugs
#14
Piotr J Kamola, Klio Maratou, Paul A Wilson, Kay Rush, Tanya Mullaney, Tom McKevitt, Paula Evans, Jim Ridings, Probash Chowdhury, Aude Roulois, Ann Fairchild, Sean McCawley, Karen Cartwright, Nigel J Gooderham, Timothy W Gant, Kitty Moores, Stephen A Hughes, Mark R Edbrooke, Kenneth Clark, Joel D Parry
Antisense oligonucleotide (ASO) gapmers downregulate gene expression by inducing enzyme-dependent degradation of targeted RNA and represent a promising therapeutic platform for addressing previously undruggable genes. Unfortunately, their therapeutic application, particularly that of the more potent chemistries (e.g., locked-nucleic-acid-containing gapmers), has been hampered by their frequent hepatoxicity, which could be driven by hybridization-mediated interactions. An early de-risking of this liability is a crucial component of developing safe, ASO-based drugs...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917147/combined-in-silico-approaches-for-the-identification-of-novel-inhibitors-of-human-islet-amyloid-polypeptide-hiapp-fibrillation
#15
Palak Patel, Krupali Parmar, Vivek K Vyas, Dhaval Patel, Mili Das
Human islet amyloid polypeptide (hIAPP) is a natively unfolded polypeptide hormone of glucose metabolism, which is co-secreted with insulin by the β-cells of the pancreas. In patients with type 2 diabetes, IAPP forms amyloid fibrils because of diabetes-associated β-cells dysfunction and increasing fibrillation, in turn, lead to failure of secretory function of β-cells. This provides a target for the discovery of small organic molecules against protein aggregation diseases. However, the binding mechanism of these molecules with monomers, oligomers and fibrils to inhibit fibrillation is still an open question...
September 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28917033/secisearch3-and-seblastian-in-silico-tools-to-predict-secis-elements-and-selenoproteins
#16
Marco Mariotti
The computational identification of selenoprotein genes is complicated by the dual meaning of the UGA codon as stop and selenocysteine. SECIS elements are RNA structures essential for selenocysteine incorporation, which have been used as markers for selenoprotein genes in many bioinformatics studies. The most widely used tool for eukaryotic SECIS finding has been recently improved to its third generation, SECISearch3. This program is also a component of Seblastian, a pipeline for the identification of selenoprotein genes that employs SECIS finding as the first step...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28916718/potential-sperm-contributions-to-the-murine-zygote-predicted-by-in-silico-analysis
#17
Panagiotis Ntostis, Deborah Carter, David Iles, J D Huntriss, Maria Tzetis, David Miller
Paternal contributions to the zygote are thought to extend beyond delivery of the genome and paternal RNAs have been linked to epigenetic transgenerational inheritance in different species. In addition, sperm-egg fusion activates several downstream processes that contribute to zygote formation, including PLC zeta-mediated egg activation and maternal RNA clearance. Since a third of the preimplantation developmental period in the mouse occurs prior to the first cleavage stage, there is ample time for paternal RNAs or their encoded proteins potentially to interact and participate in early zygotic activities...
September 15, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28916649/genomic-prediction-within-and-across-biparental-families-means-and-variances-of-prediction-accuracy-and-usefulness-of-deterministic-equations
#18
Pascal Schopp, Dominik Müller, Yvonne C J Wientjes, Albrecht E Melchinger
A major application of genomic prediction (GP) in plant breeding is the identification of superior inbred lines within families derived from biparental crosses. When models for various traits were trained within related or unrelated biparental families (BPFs), experimental studies found substantial variation in prediction accuracy (PA), but little is known about the underlying factors. We used SNP marker genotypes of inbred lines from either elite germplasm or landraces of maize (Zea mays L.) as parents to generate in silico 300 BPFs of doubled-haploid lines...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28915563/niaoduqing-granules-relieve-chronic-kidney-disease-symptoms-by-decreasing-renal-fibrosis-and-anemia
#19
Xu Wang, Suyun Yu, Qi Jia, Lichuan Chen, Jinqiu Zhong, Yanhong Pan, Peiliang Shen, Yin Shen, Siliang Wang, Zhonghong Wei, Yuzhu Cao, Yin Lu
NiaoDuQing (NDQ) granules, a traditional Chinese medicine, has been clinically used in China for over fourteen years to treat chronic kidney disease (CKD). To elucidate the mechanisms underlying the therapeutic benefits of NDQ, we designed an approach incorporating chemoinformatics, bioinformatics, network biology methods, and cellular and molecular biology experiments. A total of 182 active compounds were identified in NDQ granules, and 397 putative targets associated with different diseases were derived through ADME modelling and target prediction tools...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915445/exploring-the-association-of-rs10490924-polymorphism-with-age-related-macular-degeneration-an-in-silico-approach
#20
Farhad Jahanfar, Hamed Hamishehkar
The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. The ARMS2 gene encodes a putative small (11kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of the A69S mutation, we performed a detailed analysis of the ARMS2 sequence with a broad set of bioinformatics tools...
September 6, 2017: Journal of Molecular Graphics & Modelling
keyword
keyword
67521
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"