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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 Dec 13 2018
Journal Name
Al-adab Journal
A Victim of "Love": A Study of Beatrice’s Character in "Rappaccini's Daughter" By Nathanial Hawthorne
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Nathaniel Hawthorne (1804-1864) has been widely known for his special interest in the female characters. In many of his novels, he narrates the conditions, values, and the institutions that surround and control the life of women, leading them to be victims. In “Rappaccini’s Daughter” (1844), the heroine, Beatrice is created to be victimized by her loved ones (her father and lover). This paper focuses on the term “victim,” it shows its aspects through the development of Beatrice’s character. The paper also studies a female character in the male-dominated society, to show the cruelty done to her, and how she is considered to be a second rate person, who is unable to live normally, or at least to save herself from dea

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Publication Date
Thu Sep 02 2021
Journal Name
International Journal Of Drug Delivery Technology
Role of Lactobacillus plantarum and Lactobacillus acidophilus as a Treatment of Cryptosporidiosis in Mice
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Objective: To evaluate the therapeutic activity of probiotics mixture of Lactobacillus plantarum and Lactobacillus acidophilus towards Cryptosporidium infection in experimentally infected mice. Oocysts of Cryptosporidium were separated from the stool of humans to infect mice. Methods: Forty male albino mice were split equally into four groups, every group contained 10 mice, the group I (early treated group), were treated from the 1st day from infection to the 11th post-infection, group II (late treated group), were treated from the 4th day from infection to the 15th post-infection, and group (III) (untreated group), were mice considered as a positive control group. Results: It was showed that daily application of a mixture of L. plantarum w

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Publication Date
Sun Jan 27 2019
Journal Name
Civil Engineering Journal
Prediction of Sediment Accumulation Model for Trunk Sewer Using Multiple Linear Regression and Neural Network Techniques
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Sewer sediment deposition is an important aspect as it relates to several operational and environmental problems. It concerns municipalities as it affects the sewer system and contributes to sewer failure which has a catastrophic effect if happened in trunks or interceptors. Sewer rehabilitation is a costly process and complex in terms of choosing the method of rehabilitation and individual sewers to be rehabilitated.  For such a complex process, inspection techniques assist in the decision-making process; though, it may add to the total expenditure of the project as it requires special tools and trained personnel. For developing countries, Inspection could prohibit the rehabilitation proceeds. In this study, the researchers propos

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Publication Date
Sat Dec 31 2022
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of Robust Circular S and Circular Least Squares Estimators for Circular Regression Model using Simulation
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In this paper, the Monte-Carlo simulation method was used to compare the robust circular S estimator with the circular Least squares method in the case of no outlier data and in the case of the presence of an outlier in the data through two trends, the first is contaminant with high inflection points that represents contaminant in the circular independent variable, and the second the contaminant in the vertical variable that represents the circular dependent variable using three comparison criteria, the median standard error (Median SE), the median of the mean squares of error (Median MSE), and the median of the mean cosines of the circular residuals (Median A(k)). It was concluded that the method of least squares is better than the

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Publication Date
Mon Apr 17 2017
Journal Name
Wireless Personal Communications
ITPMAP: An Improved Three-Pass Mutual Authentication Protocol for Secure RFID Systems
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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of King Saud University - Science
Three iterative methods for solving second order nonlinear ODEs arising in physics
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Publication Date
Tue Feb 01 2022
Journal Name
Baghdad Science Journal
Impact of Culture Media Composition, Nutrients Stress and Gamma Radiation on Biomass and Lipid of the Green Microalga, Dictyochloropsis splendida as a Potential Feedstock for Biodiesel Production
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Biodiesel production from microalgae depends on the biomass and lipid production. Both biomass and lipid accumulation is controlled by several factors. The effect of various culture media (BG11, BBM, and Urea), nutrients stress [nitrogen (N), phosphorous (P), magnesium (Mg) and carbonate (CO3)] and gamma (γ) radiation on the growth and lipid accumulation of   Dictyochloropsis splendida were investigated. The highest biomass and lipid yield of D. splendida were achieved on BG11 medium. Cultivation of D. splendida in a medium containing 3000 mg L−1 N, or 160 mg L−1 P, or 113 mg L−1 Mg, or 20 mg L-1 CO3, led to enhanced growth rate. While u

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Publication Date
Mon May 09 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Choosing the Planning Aggregate Production strategy of the Organization of service - A Case Study in Baghdad hotel: Choosing the Planning Aggregate Production strategy of the Organization of service - A Case Study in Baghdad hotel
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Constitute a planning problem on the basis of personal experience and self-governance in the service organizations away from quantitative scientific method in planning an anchor and a platform, who made a recent research study, analysis and interpretation through scientific methodology adopted which formed its contents, The research aims to identify the true reality of production planning in service organizations, specifically in the Baghdad Hotel as a society to look, in order to assess the best strategy through the standard cost of the strategies of tracking and settlement to cope with developments on services demand changes, Search results confirmed that the settlement rates of production strategy is the best strategy in accordance wi

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Publication Date
Thu Jul 01 2021
Journal Name
International Journal Of Nonlinear Analysis And Application
Forecasting enhancement using a hodrick-prescott filter
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: Sound forecasts are essential elements of planning, especially for dealing with seasonality, sudden changes in demand levels, strikes, large fluctuations in the economy, and price-cutting manoeuvres for competition. Forecasting can help decision maker to manage these problems by identifying which technologies are appropriate for their needs. The proposal forecasting model is utilized to extract the trend and cyclical component individually through developing the Hodrick–Prescott filter technique. Then, the fit models of these two real components are estimated to predict the future behaviour of electricity peak load. Accordingly, the optimal model obtained to fit the periodic component is estimated using spectrum analysis and Fourier mod

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Publication Date
Sun Sep 24 2023
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Human Recognition Using Ear Features: A Review
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Over the past few years, ear biometrics has attracted a lot of attention. It is a trusted biometric for the identification and recognition of humans due to its consistent shape and rich texture variation. The ear presents an attractive solution since it is visible, ear images are easily captured, and the ear structure remains relatively stable over time.  In this paper, a comprehensive review of prior research was conducted to establish the efficacy of utilizing ear features for individual identification through the employment of both manually-crafted features and deep-learning approaches. The objective of this model is to present the accuracy rate of person identification systems based on either manually-crafted features such as D

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