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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Thu Jun 28 2018
Journal Name
2018 4th International Conference On Computer And Technology Applications (iccta)
Improving accuracy of CADx system by hybrid PCA and backpropagation
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—Medical images have recently played a significant role in the diagnosis and detection of various diseases. Medical imaging can provide a means of direct visualization to observe through the human body and notice the small anatomical change and biological processes associated by different biological and physical parameters. To achieve a more accurate and reliable diagnosis, nowadays, varieties of computer aided detection (CAD) and computer-aided diagnosis (CADx) approaches have been established to help interpretation of the medical images. The CAD has become among the many major research subjects in diagnostic radiology and medical imaging. In this work we study the improvement in accuracy of detection of CAD system when comb

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Publication Date
Wed May 08 2024
Journal Name
Journal Of Mathematics And Computer Science
How does media coverage affect a COVID-19 pandemic model with direct and indirect transmission?
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In this paper, a compartmental differential epidemic model of COVID-19 pandemic transmission is constructed and analyzed that accounts for the effects of media coverage. The model can be categorized into eight distinct divisions: susceptible individuals, exposed individuals, quarantine class, infected individuals, isolated class, infectious material in the environment, media coverage, and recovered individuals. The qualitative analysis of the model indicates that the disease-free equilibrium point is asymptotically stable when the basic reproduction number R0 is less than one. Conversely, the endemic equilibrium is globally asymptotically stable when R0 is bigger than one. In addition, a sensitivity analysis is conducted to determine which

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Publication Date
Sat Jul 30 2022
Journal Name
Global Academic Journal Of Linguistics And Literature
A Critical Stylistic Analysis of Transcultural Identity in Lyer’s The Global Soul (2001) Using the Tool of Negation
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This study is intended to examine the concept of transcultural identity in the travel book The Global Soul: Jet Lag, Shopping Malls, and the Search for Home by (Iyer, 2001). Jeffries’ model of critical stylistics (2010) (henceforth, CS) has been selected to analyze the book. To be more specific, Negation is selected to analyze the concept under study. As such, the study aims at finding out how Negation is used to portray ideological meanings representing the concept of transcultural identity in one non-fictional travel book; and finding out the ideologies related to the concept analyzed. The analysis of the data shows that Negation is a suitable analytical tool to reach the ideational meaning of the text towards the concept of tra

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Publication Date
Mon Mar 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
Pais estimator for the reliability function of the Pareto model of Type I failure
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In this paper an estimator of reliability function for the pareto dist. Of the first kind has been derived and then a simulation approach by Monte-Calro method was made to compare the Bayers estimator of reliability function and the maximum likelihood estimator for this function. It has been found that the Bayes. estimator was better than maximum likelihood estimator for all sample sizes using Integral mean square error(IMSE).

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Publication Date
Tue Mar 30 2021
Journal Name
Baghdad Science Journal
Diversity Assessment by Molecular Barcoding and Seed Morphology in Ricinus communis L.: Molecular diversity of Ricinus seeds
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Fourteen morphologically varied Ricinus communis L. seeds were collected from different localities in Egypt, El-Sudan and Saudi Arabia. Seed morphology and ITS barcoding analysis were performed to assess their diversity and phylogenetic relationship. Sequence’s alignment of nrITS region from different accessions display high levels of genetic similarities. Cluster analysis could not group different accessions according to their geographical distribution. Nevertheless, the genetic barcodes are interestingly matched with the morphological features of the Ricinus seeds. In conclusion, seed morphology proved to be a valuable tool in evaluating biodiversity and phylogenetic relationship in plant species with different loca

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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of Research In Medical And Dental Science
The Efficacy of 4% Articaine Infiltration Anesthesia in the Extraction of Mandibular Molars: A Randomized Controlled Study
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Introduction: Articaine was developed in 1969, with reported advantages which are increased potency, increased duration of its anesthetic effect and superior diffusion through bony tissue. The effectiveness of using 4% articaine infiltration for extraction of mandibular molar teeth in comparison to 2% lidocaine inferior alveolar nerve block is not settled yet. Aim: The aim of this study was to evaluate the effectiveness of using 4% articaine infiltration for extraction of mandibular molars by comparing it to the use of 2% lidocaine inferior alveolar nerve block in terms of success, the volume of local anesthetic agents and the pain experienced during the procedure. Materials and methods: A prospective randomized controlled study included

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Publication Date
Tue Dec 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
The role of MIS in the negotiation process "An Analytical Study in a Sample of Iraqi Organizations"
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Negotiation is considered as one of the most important kinds of communication in the contemporary organizations, which depend on the important role of managerial information systems in providing necessary and suitable information for success of the negotiation process.

Accordingly, this study aims at measuring the extent of the variables effect of managerial information system in the negotiation process.

To achieve this study, two hypotheses were chosen; the first is the correlation relation and the second is the effect, and statistical means represented by correlation coefficient "Spearman" and (R2) were used.

 A Number of conclusions were

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Publication Date
Wed Feb 22 2023
Journal Name
Iraqi Journal Of Agricultural Sciences
A STUDY OF ECONOMIC, SOCIAL, AND INSTITUTIONAL FACTORS AFFECTING THE ADOPTION OF THE HIGH-RANK WHEAT SEEDS
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The aim of this research is to investigate the effect of economic, social and institutional factors on adoption within the national program for the propagation of high-rank seeds of wheat crop. 170 questionnaires were collected, 50% of them were participants in the program from Wasit and Babil governorates. Probabilistic regression models were used to know this effect, and the possibility of adopting Farmers of improved seeds produced from the national program for the multiplication of seeds of higher grades using the (ADOPT) program. The adoption rate was 0.12%, and the total number of adopters were 12 farmers, at a rate of 14.2%. Tobit model was estimated  to find out the impact of the profitability of the dunum, capital, farm si

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Publication Date
Wed Dec 15 2021
Journal Name
Al-academy
The role of psychological content in building the fiction film an analytical study of a selected sample
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 Psychological aspects are a major influence and motivation factor in many cinematic and television works such as television series. There are many films that dealt with psychological issues through the personality affected by psychological projections and complexes that lead towards abnormal behavior and actions in most cases, so the researchers chose the title and the research problem was raised through the following question: What is the mechanism that fulfills a psychological role in the narrative film? The objectives of the research were to reveal the mechanism used to instill psychological contents in the feature film? As for the limits of the research, it was an intentional sample, and the researchers adopted the descriptive anal

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Engineering
Experimental Evaluation Use of Semifluidized Bed Adsorber for the Treatment of P-chlorophenol and O-cresol in Wastewater using Activated Carbon as Adsorbent
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In the present work the performance of semifluidized bed adsorber was evaluated for removal of phenolic compound from wastewater using commercial activated carbon as adsorbent. P-chlorophenol (4-Chlorophenol) and o-cresol (2-methylphenol) was selected as a phenolic compound for that purpose. The phenols percent removal, in term of breakthrough curves were studied as affected by hydrodynamics limitations which include minimum and maximum semifluidization velocities and packed bed formation in the column by varying various parameters such as inlet liquid superficial velocity (from Uminsf to 8Uminsf m/s), and retaining grid (sometimes referred to as adsorbent loading) to initial static bed height ratio (from 3-4.5). In

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