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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 Jan 01 2019
Journal Name
Annals Of Tropical Medicine And Public Health
Arlyesterase activity of Paraoxonase-1 enzyme in Iraqi patients with β-thalassemia minor
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Background: Arylesterase activity of Paraoxonase-1 (ARE-PON-1) exhibits an antioxidant role which protects lipoprotein from oxidation. It is known that ARE-PON-1 antioxidant activity associated with high density lipoprotein cholesterol (HDL-C) reduces the oxidative damage mediated by low density lipoprotein cholesterol (LDL-C). The present study was aimed to examine the level of serum ARE-PON1 in Iraqi patients with β-thalassemia minor and its relationship with lipid profile (total cholesterol (TC), HDL-C, very low density lipoprotein (VLDL-C), and LDL-C) and hematologic changes as a part of antioxidant system action. Methods: In the present study, the ARE-PON-1 activity was investigated in serum of patients with β-thalassemia minor. Resu

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Publication Date
Fri Nov 29 2019
Journal Name
Iraqi Journal Of Physics
Gas Sensing of (SnO2)1-x(ZnO)x Composite Associating with Electrical Properties
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Abstract

Semiconductor-based gas sensors were prepared, that use n-type tin oxide (SnO2) and  tin oxide: zinc oxide composite (SnO2)1-x(ZnO)x at different x ratios using pulse laser deposition at room temperature. The prepared thin films were examined to reach the optimum conditions for gas sensing applications, namely X-ray diffraction, Hall effect measurements, and direct current conductivity. It was found that the optimum crystallinity and maximum electron density, corresponding to the minimum charge carrier mobility, appeared at 10% ZnO ratio. This ratio appeared has the optimum NO2 gas sensitivity for 5% gas concentration at 300 °C working temperat

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Publication Date
Fri Mar 31 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Micro encapsulation of Naproxen By Complex Coacervation and Aqueous Colloid Dispersion Part ( 1 )
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Naproxen is a non steroidal anti inflammatory and antipyretic drug which has local irritation effect  on  the  stomach, and  unpleasant taste,  besides bad   flowability and light sensitivity .The drug was prepared as microcapsules by complex coacervation method using acacia-gelatin coating materials , and aqueous colloid polymer dispersion method ( ACPD ), using ethyl cellulose and sodium alginate coating materials . The results indicated that microcapsules prepared by 2:1  core:wall ratio is the best for both methods, with an average encapsulation efficiency (75%) and avarege yield (90%) .

Moreover the drug release was affected mainly by core : ratio ,pH enviroment and method of microenca

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Publication Date
Mon Feb 06 2023
Journal Name
Journal Of Toxicology
Zinc Chloride Can Mitigate the Alterations in Metallothionein and Some Apoptotic Proteins Induced by Cadmium Chloride in Mice Hepatocytes: A Histological and Immunohistochemical Study
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The heavy metal cadmium is extremely harmful to both humans and animals. Zinc supplementation protects the biological system and reduces cadmium-induced toxicity. This study aimed to determine whether zinc chloride (ZnCl2) could protect male mice with the damaged liver induced by cadmium chloride (CdCl2). The protective role of zinc chloride and expression of the metallothionein (MT), Ki-67, and Bcl-2 apoptotic proteins in hepatocytes were studied after subchronic exposure of mice to cadmium chloride for 21 days. Thirty male mice were randomly categorized into 6 groups (5 mice/group) as follows: a control group that did not receive any treatment, a group given ZnCl2 at 10 mg/kg alone, and two groups received ZnCl2 (10 mg/kg) i

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Publication Date
Wed Aug 29 2018
Journal Name
Biomedical And Pharmacology Journal
Comparison of Some Mechanical and Physical Properties of three Types of Impression Materials with Different Dental Implant Angulations
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Choosing an appropriate impression material is a challenge for many dentists, yet an essential component to provide an excellent clinical outcome and improve productivity and profit. The purpose of present study was to compare wettability, tear strength and dimensional accuracy of three elastomeric impression materials, with the same consistencies (light-body). Three commercially available light body consistency and regular set 3M ESPE Express polyvinylsiloxane (PVS), 3M ESPE Permadyne polyether (PE), and Identium (ID), impression materials were comparedTear strength test, contact angle test and linear dimensional accuracy were evaluated for three elastic impression material. Among the three experimental groups PE impression materia

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Publication Date
Fri May 30 2025
Journal Name
Iraqi Journal Of Science
A Novel Approach for Synthesizing the Pan-chromatic Band to (10 m) of Landsat 9 Based on Sentinel-2 Data to Improve Classification Performance
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This study investigates the impact of spatial resolution enhancement on supervised classification accuracy using Landsat 9 satellite imagery, achieved through pan-sharpening techniques leveraging Sentinel-2 data. Various methods were employed to synthesize a panchromatic (PAN) band from Sentinel-2 data, including dimension reduction algorithms and weighted averages based on correlation coefficients and standard deviation. Three pan-sharpening algorithms (Gram-Schmidt, Principal Components Analysis, Nearest Neighbour Diffusion) were employed, and their efficacy was assessed using seven fidelity criteria. Classification tasks were performed utilizing Support Vector Machine and Maximum Likelihood algorithms. Results reveal that specifi

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Publication Date
Fri Jul 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Determine the best model to predict the consumption of electric energy in the southern region
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Abstract:          

                Interest in the topic of prediction has increased in recent years and appeared modern methods such as Artificial Neural Networks models, if these methods are able to learn and adapt self with any model, and does not require assumptions on the nature of the time series. On the other hand, the methods currently used to predict the classic method such as Box-Jenkins may be difficult to diagnose chain and modeling because they assume strict conditions.

  

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Publication Date
Sat May 05 2012
Journal Name
Journal Of Planner And Development
planning and design of a tourist village in the marshes of southern Iraq
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This study analyzes how to make use of the resources in the marshlands of Iraq and how to utilize them, especially after the water returns to these areas and they are revitalized. We take an example of AL- Saheen Marsh and plan an ideal tourist resort there. This example can further expand to include other parts of the marshlands. The resort will utilize the local environment and tourist characteristics as it will have a feel and architectural resemblance to the houses and buildings that are currently built there. In addition the transportation methods will be the same as those used by the locals. Yet the resort will still posses all the facilities required by a modern tourist resort that includes all the services that will make

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Publication Date
Wed Apr 24 2019
Journal Name
Aerosol Science And Technology
Effect of axial eccentricity on the performance of a cylindrical differential mobility classifier
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Publication Date
Sun Apr 01 2018
Journal Name
Academy Of Accounting And Financial Studies Journal
Factors influence the growth and penetration of microfinance institutions: A case of Egypt
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Microfinance Institutions (MFIs) offers small loans with easy repayment system and till now these institutions have served millions of needy people around the globe. This study highlights the hurdles influence the smooth working and growth of Microfinance institution in Egypt. The structured interviews were conducted from the top and mid-level managers of MFI's. This study revealed that interest rate, political and economic conditions, corruption, customer outreach, competition and technology are the important elements for MFI's success. It is evident that lack of use of technology and less importance drawn on customer outreach programs are the main challenges of MFI's in Egypt. This study provides a roadmap for practitioners and strategic

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