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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 Feb 01 2024
Journal Name
Surface Engineering And Applied Electrochemistry
Synthesis of New 1,2,4-Triazole Containing Copolymers and Their Corrosion Inhibition оf Mild Steel in Acidic Medium
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Publication Date
Wed Dec 12 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Effectiveness of Education Program on Health Care Workers’ Practices toward Waste Management in Primary Health Care Centers
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Objective(s): The aim of this study is to determine the effectiveness of education program on Health Care Workers’ practices toward Primary Health Care Centers waste management and to identify the relationship between these practices and the demographic characteristics of the health workers. Methodology: A quasi- experimental design (pre-post tests) has been used in the present study for the period of November 16th 2014 to June 22nd 2015 .The allocated sample in the present study is consisted of (60) health care worker. The sample was randomly divided into two groups of (30) health care workers each. The stu

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Publication Date
Wed May 01 2019
Journal Name
Journal Of Engineering
Optimization of Friction Stir Welding Process Parameters to joint 7075-T6 Aluminium Alloy by Utilizing Taguchi Technique
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In this study, a 3 mm thickness 7075-T6 aluminium alloy sheet was used in the friction stir welding process. Using the design of experiment to reduce the number of experiments and to obtain the optimum friction stir welding parameters by utilizing Taguchi technique based on the ultimate tensile test results. Orthogonal array of L9 (33) was used based on three numbers of the parameters and three levels for each parameter, where shoulder-workpiece interference depth (0.20, 0.25, and 0.3) mm, pin geometry (cylindrical thread flat end, cylindrical thread with 3 flat round end, cylindrical thread round end), and thread pitch (0.8, 1, and 1.2) mm) this technique executed by Minitab 17 software. The results showed th

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Publication Date
Mon Apr 04 2016
Journal Name
Iraqi Journal Of Physics
Thickness and gamma-ray effect on physical properties of CdO thin films grown by pulsed laser deposition
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Polycrystalline Cadmium Oxide (CdO) thin films were prepared using pulsed laser deposition onto glass substrates at room temperature with different thicknesses of (300, 350 and 400)nm, these films were irradiated with cesium-137(Cs-137) radiation. The thickness and irradiation effects on structural and optical properties were studied. It is observed by XRD results that films are polycrystalline before and after irradiation, with cubic structure and show preferential growth along (111) and (200) directions. The crystallite sizes increases with increasing of thickness, and decreases with gamma radiation, which are found to be within the range (23.84-4.52) nm and (41.44-4.974)nm before and after irradiation for thickness 350nm and 4

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Publication Date
Wed Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
Job satisfaction in motivating potential energy of youth charged and non-enforcement officials' relationship newly administrative work
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The good preparation for a class of young people is the great importance requirement.
This case on the state role to put exceptional philosophy bench form which the entire category
through group of experienced educators to prepare different and distinct programs to suit
every specialty of this class. This base of this role can draw upon, including state institutions
need of young people add urges the mental and physical abilities, scientific and cognitive
specialties and carry it from the levee in the academic certification .And we must not lose the
lose sight of the link that pilot projects in which to invest the energies of youth programs and
curricula attractions including incentives .It's become the subject of jo

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation Status Of Central Laboratories In Al- Kadhimya Teaching Hospital According To ISO/IEC 17025 In 2005
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This research aims to analyze and evaluate  the reality of the total quality management for the central laboratories by comparing systems of work in the laboratories of Al- Kadhimiya Didactic Hospital with the requirements of ISO 17025 to determine the degree of compatibility and the willingness to adapt to the requirements of the above specification and to show the ability of building an applicable quality management system and to identify problems and their mitigations and prevention to increase.

This study gains its importance from the importance of the labs which stems from the fact that the process of health is a set of interrelated activities, Medical examinations and tests con

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Publication Date
Thu Nov 21 2019
Journal Name
Al-kindy College Medical Journal
Effect Of Pomegrante Peels And Bay Leaves On Multidrug Resistant Bacteria Isolated From Urinary Tract Infection Patients
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Background: Alternative natural therapy by plants extracts had opened  wide  door   for   the    use  of  natural products as an alternative therapy instead of many antibiotics and drugs , which had many harmful side effects.Also, an increased interest has been centered on the industrial wastes, especially plant raw materials which contain phenols (e.g. Pomegranate peel and Bay leaves) which is a sources of natural antioxidants ,which are on the contrary  of  synthetic  antioxidants that  had restrict use  due to  their  health  risks , carcinogenesis and toxicity .

Objectives :This study was done to fi

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Publication Date
Sat Jul 01 2023
Journal Name
Chemical Methodologies
Acid Activation of Iraqi Bentonite Clay and Studying its Structural, Dielectric and Electrical Behavior at Various Temperatures
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Iraqi calcium bentonite was activated via acidification to study its structural and electrical properties. The elemental analysis of treated bentonite was determined by using X-ray fluorescence while the unit crystal structure was studied through X-ray diffraction showing disappearance of some fundamental reflections due to the treatment processes. The surface morphology, on the other hand, was studied thoroughly by Scanning Electron microscopy SEM and Atomic Force Microscope AFM showing some fragments of montmorillonite sheets. Furthermore, the electrical properties of bentonite were studied including: The dielectric permittivity, conductivity, tangent loss factor, and impedance with range of frequency (0.1-1000 KHz) at different temperatu

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Publication Date
Sun Jun 26 2022
Journal Name
Electrical Engineering
Optimal insulation design of form-wound stator winding with stress grading system under fast rise-time excitation
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The effective insulation design of the stress grading (SG) system in form-wound stator coils is essential for preventing partial discharges and excessive heat generation under pulse-width modulation excitation. This paper proposes a method to find the optimal insulation design of the SG system aimed at reducing the dielectric and thermal stresses in the machine coil. The non-uniform transmission line model is used to predict the voltage propagation along the overhang, SG, and slot regions considering the variation in the physical properties of the insulation layers. The machine coil parameters for different insulation materials are calculated by using the finite element method. Two optimization algorithms, fmincon and particle swarm optimiz

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Publication Date
Sun May 15 2022
Journal Name
Revistabionatura
Synthesis and characterization of azo liquid crystal compounds based on 5H-Thiazolo [3,4-b][1,3,4] thiadiazole unit
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A calamitic symmetric liquid crystalline consisting of an azo group containing 5H-Thiazolo[3,4-b][1,3,4]thiadiazole moiety compound[III] was synthesized via sequence reactions starting from reaction terephthaldehyde with mercaptoacetic acid and thiosemicarbazide in the presence of concentrated sulfuric acid to synthesized 5,5'-(1,4-phenylene)bis(5Hthiazolo[4,3-b][1,3,4]thiadiazol-2-amine)[I] then the azo compound [II] synthesized by coupling between diazonium salt of the compound [I] with phenol at (0-4) ̊C., after that the compound [III] was synthesized by the reaction of the compound [II] with methyl bromide in alkaline media. The compounds are characterized by melting points, FTIR and 1HNMR spectroscopy. The mesomorphic behavior was stu

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