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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
Tue Feb 28 2023
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Bitcoin Prediction with a hybrid model
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. In recent years, Bitcoin has become the most widely used blockchain platform in business and finance. The goal of this work is to find a viable prediction model that incorporates and perhaps improves on a combination of available models. Among the techniques utilized in this paper are exponential smoothing, ARIMA, artificial neural networks (ANNs) models, and prediction combination models. The study's most obvious discovery is that artificial intelligence models improve the results of compound prediction models. The second key discovery was that a strong combination forecasting model that responds to the multiple fluctuations that occur in the bitcoin time series and Error improvement should be used. Based on the results, the prediction a

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Publication Date
Tue Apr 01 2025
Journal Name
Journal Of Economics And Administrative Sciences
Spatial Quantile Autoregressive Model: A Review
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This paper is specifically a detailed review of the Spatial Quantile Autoregressive (SARQR) model that refers to the incorporation of quantile regression models into spatial autoregressive models to facilitate an improved analysis of the characteristics of spatially dependent data. The relevance of SARQR is emphasized in most applications, including but not limited to the fields that might need the study of spatial variation and dependencies. In particular, it looks at literature dated from 1971 and 2024 and shows the extent to which SARQR had already been applied previously in other disciplines such as economics, real estate, environmental science, and epidemiology. Accordingly, evidence indicates SARQR has numerous benefits compar

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Publication Date
Fri Mar 12 2021
Journal Name
Medico Legal Update
Human Cytomegalovirus Infection as a Risk Factor for Type 2 Diabetes Mellitus Development in a Sample of Iraqi Patients
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Type 2 diabetes mellitus which abbreviate as T2DM is a complex endocrine and metabolic disorder arisingfrom genetic and environmental factors interaction which in turn induce various degrees of insulin functionalalteration on peripheral tissues. Globally, T2DM has develop into a public health problem. Therefore, Thestudy included (75) patients(37 female and 38 males) suffering from T2DM who visit al-kadhimiya teachinghospital with age range 20-80 years and (70) as healthy controls with age range 20-70 years. All studiedgroups were evaluated CMV IgG by ELISA,B. urea, S. Creatinine, cholesterol and triglyceride the resultsshowed that B.urea, S.creatinine and serum cholesterol showed a non-significant differences between studiedgroup,

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Publication Date
Tue Aug 02 2022
Journal Name
International Journal Of Research In Social Sciences & Humanities
The Making of a Heroine: A Female Character as Portrayed in The English Patient By Michael OndaatjE
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This article discusses how women have significant abilities to cope with the difficulties of war times. They are not the weak and vulnerable victims who are thought to be. On the contrary, they have the power to control over many-sided fronts, like participating in the battlefield as nurses or activists for peace, or even fighters, as well as through the tasks and responsibilities assigned to them to protect and support their families during wartime. The researcher will examine the impact of war upon women. Like men, women suffer during wartime. They are being injured, tortured and killed. Yet, they are able to give examples of love and courage even in the difficult times of war. Hana is one of those women who lived during wartimes,

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Publication Date
Thu Dec 01 2022
Journal Name
Baghdad Science Journal
A Green Synthesis of Iron/Copper Nanoparticles as a Catalytic of Fenton-like Reactions for Removal of Orange G Dye
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This research paper studies the use of an environmentally and not expensive method to degrade Orange G dye (OG) from the aqueous solution, where the extract of ficus leaves has been used to fabricate the green bimetallic iron/copper nanoparticles (G-Fe/Cu-NPs). The fabricated G‑Fe/Cu-NPs were characterized utilizing scanning electron microscopy, BET, atomic force microscopy, energy dispersive spectroscopy, Fourier-transform infrared spectroscopy and zeta potential. The rounded and shaped as like spherical nanoparticles were found for G-Fe/Cu‑NPs with the size ranged 32-59 nm and the surface area was 4.452 m2/g. Then the resultant nanoparticles were utilized as a Fenton-like oxidation catalyst. The degradation efficiency of

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Publication Date
Thu Jun 16 2022
Journal Name
Comparative Parasitology
A Comparative Study of Some Intestinal Parasites in Fecal Samples of Domestic and Stray Cats in Baghdad, Iraq
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Some feline intestinal parasites such as Toxocara, Giardia, and Cryptosporidium can spread to humans through feces. Therefore, it is important to prevent exposure of family members by screening cat fecal samples twice per year for potential treatment regimes. This study was initiated to compare and identify gastrointestinal parasites of domestic and stray cats (Felis domesticus) in Baghdad City, Iraq. Parasite eggs and oocysts were identified under light microscopy by applying standard laboratory techniques (flotation and sedimentation). Overall, 59 of 121 (48.7%) fecal samples were positive for intestinal parasites. The rate of infection by Toxoplasma gondii was (3.31%), Isospora spp. (6.61%), Cryptosporidium spp. (31.4%), and Toxocara spp

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Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Us-china Public Administration
Victims of Terrorism between Compensation and Loss of Rights: A Comparative Study between Iraqi Law and French Law
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The problem of the damage caused by terrorist acts has raised many difficulties in many countries, including Iraq, which requires the existence of a law that sets out sufficient rules for compensating the victims of terrorist acts, in order to compensate them for the harm they have not suffered. It may be difficult or impossible for them to identify causing damage, and therefore unable to obtain compensation by applying the traditional rules of liability that require proof of fault and identify the culprit. The security funds come as an appropriate alternative that pays compensation in such cases for victims to reparation for the damage they suffered. Therefore, this problem remains one of the most problems that Iraq suffers from it, which

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Publication Date
Mon Dec 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Comparative Study of Pressure Losses and Hole Cleaning Efficiency of Water and Polymer solutions in Horizontal Wells
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The main objective of this study is to experimentally investigate the effect of the CMC polymeric drag reducer on the pressure drop occurred along the annulus of the wellbore in drilling operation and investigate the optimum polymer concentration that give the minimum pressure drop. A flow loop was designed for this purpose consist from 14 m long with transparent test section and differential pressure transmitter that allows to sense and measure the pressure losses along the test section. The results from the experimental work show that increasing in polymer concentration help to reduce the pressure drop in annulus and the optimum polymer concentration with the maximum drag reducing is 0.8 kg/m3. Also increasing in flow rate a

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Publication Date
Mon Jan 13 2020
Journal Name
Day 3 Wed, January 15, 2020
Numerical Simulation of Gas Lift Optimization Using Genetic Algorithm for a Middle East Oil Field: Feasibility Study
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<p>Gas-lift technique plays an important role in sustaining oil production, especially from a mature field when the reservoirs’ natural energy becomes insufficient. However, optimally allocation of the gas injection rate in a large field through its gas-lift network system towards maximization of oil production rate is a challenging task. The conventional gas-lift optimization problems may become inefficient and incapable of modelling the gas-lift optimization in a large network system with problems associated with multi-objective, multi-constrained, and limited gas injection rate. The key objective of this study is to assess the feasibility of utilizing the Genetic Algorithm (GA) technique to optimize t</p> ... Show More
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Publication Date
Thu Jun 01 2017
Journal Name
International Journal Of Applied Engineering Research
A Proposed Method for Generating a Private Key Using Digital Color Image Features
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In this paper, the goal of proposed method is to protect data against different types of attacks by unauthorized parties. The basic idea of proposed method is generating a private key from a specific features of digital color image such as color (Red, Green and Blue); the generating process of private key from colors of digital color image performed via the computing process of color frequencies for blue color of an image then computing the maximum frequency of blue color, multiplying it by its number and adding process will performed to produce a generated key. After that the private key is generated, must be converting it into the binary representation form. The generated key is extracted from blue color of keyed image then we selects a c

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