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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
Sun Dec 30 2018
Journal Name
Journal Of Engineering
A Cognition Path Planning with a Nonlinear Controller Design for Wheeled Mobile Robot Based on an Intelligent Algorithm
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This paper presents a cognition path planning with control algorithm design for a nonholonomic wheeled mobile robot based on Particle Swarm Optimization (PSO) algorithm. The aim of this work is to propose the circular roadmap (CRM) method to plan and generate optimal path with free navigation as well as to propose a nonlinear MIMO-PID-MENN controller in order to track the wheeled mobile robot on the reference path. The PSO is used to find an online tune the control parameters of the proposed controller to get the best torques actions for the wheeled mobile robot. The numerical simulation results based on the Matlab package show that the proposed structure has a precise and highly accurate distance of the generated refere

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Publication Date
Mon Nov 24 2025
Journal Name
Al–bahith Al–a'alami
The role of Iraqi newspapers in instilling political culture among the public after 2003, a field study on the audience of the city of Baghdad
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The role of Iraqi newspapers in instilling political culture among the public after 2003, a field study on the audience of the city of Baghdad, University of Baghdad, College of Information, Department of Journalism, 2019,
The problem of research is to investigate the role of Iraqi newspapers in instilling the political culture of individuals after 2003, and monitor this role Through the contents and messages provided by the Iraqi newspapers to the public. the research is classified within descriptive research, it adopts the survey methodology and used the questionnaire tool. In fact, the questionnaire was distributed to a sample of 400 individuals that was selected according to the method of multi-stage cluster sample of those who re

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Physical Education
The effect of the Perkins-Blyth model on learning some compound skills in soccer for second intermediate students
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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
Fabrication and characterization of zinc oxide nanorods coated by graphene oxide ZnO-NR@GO as a potential hybrid material photocatalyst
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Hybrid architecture of ZnO nanorods/graphene oxide ZnO-NRs@GO synthesized by electrostatic self-assembly methods. The morphological, optical and luminescence characteristics of ZnO-NRs@GO and ZnO-NRs thin films have been described by FESEM, TEM, HRTEM, and AFM, which refers to graphene oxide have been coated ZnO-NRs with five layers. Here we synthesis ZnO-NRs@GO by simple, cheap and environmentally friendly method, which made it favorable for huge -scale preparation in many applications such as photocatalyst. ZnO-NRs@GO was applied as a photocatalyst Rodamin 6 G (R6G) dye from water using 532 nm diode laser-induced photocatalytic process. Overall degradation of R6G/ ZnO-NRs@GO was achieved after 90 minutes of laser irradiation while it ne

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Publication Date
Thu Jun 30 2022
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
EFFECT OF USING STEVIA LEAF POWDER IN THE MANUFACTURE OF A DAIRY PRODUCT (CREAM) AGAINST THE MICROORGANISMS THAT CAUSE FOOD SPOILAGE AND THEIR ACCEPTANCE BY THE CONSUMER: EFFECT OF USING STEVIA LEAF POWDER IN THE MANUFACTURE OF A DAIRY PRODUCT (CREAM) AGAINST THE MICROORGANISMS THAT CAUSE FOOD SPOILAGE AND THEIR ACCEPTANCE BY THE CONSUMER
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The increase in obesity and the many accompanying diseases is attributed to the increased production and consumption of foods made of non-nutritive sweeteners without regard to the risks of consuming additional calories, and this in turn leads to hormonal imbalance and metabolic disorders and the resulting imbalance and ill health that have spread to all segments of society. During the research, 0.01, 0.02, 0.03, 0.04 and 0.05 % of stevia sweetener was added to the cream instead of the sugar used. Physical and chemical tests were performed for the stevia extract and the microbial content in the cream, as well as the sensory evaluation. It was noted that fortifying the cream with calorie-free stevia sugar led to the production of

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Publication Date
Fri Jul 02 1999
Journal Name
Iraqi Journal Of Science
A new proposal method for sampling and explosion of the phosphatic rocks in the Akkashat Mine, Western desert, Iraq
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Publication Date
Wed Mar 29 2023
Journal Name
Journal Of The College Of Education For Women
The Omani Sultanate of Zanzibar between Unity and Separation for the Period between (1223-1275 AH/ 1806-1861 A)
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Sultan Said bin Sultan bin Ahmed bin Said Al-Busaidi (1223-1273 AH / 1806-1856 AD) was able to rule Oman and Zanzibar in a unified Arab-African state during his reign. However, it was separated for several reasons. Thus, the study aims to clarify the efforts made by Sultan Said for annexing Zanzibar to Oman, establishing the Arab-African Sultanate, and shedding light on the role played by Britain in dividing the Arab-African Sultanate and separating Zanzibar from the Omani rule in (1275 AH-1861 AD). The study has adopted the historical descriptive analytical approach. The study has reached several conclusions, such as: The economic motivators  were the most important factors that pushed Sultan Said to move his capital from Muscat to

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
The Effect of LED Light on Depth of Cure and Microhardness of Three Types of Bulkfill Composite
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Background: To evaluate the ISO depth of cure of bulkfill composites and depth of cure which determined by Vickers microhardness test. Materials and Methods: Bulkfill resin composite specimens (n=150) were prepared of three bulkfill composite materials (TetricEvo Ceram, Quixfil and SDR) and light cured by Flash max p3 for 3, 10, 20 seconds and by wood pecker for 10, 20 seconds respectively, a mold was filled with one of the three bulkfill composites and light cured. The specimens removed from the mold and scraped by plastic spatula and the remaining length (absolute length) was measured which represent the ISO depth of cure. After that the specimens were returned into the mold and a microhardness indentation device applied on the specimen

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Publication Date
Thu Feb 07 2019
Journal Name
Iraqi Journal Of Laser
Investigation of Nonlinear Optical Characteristics of the Multi-Wall Carbon Nanotubes (MWCNT's) Suspensions using Nonlinear Self-Diffraction of a Laser Beam
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Nonlinear diffraction patterns can be obtained by focusing a laser beam through a thin slice of the material. Here, we investigated experimentally the formation of the far field nonlinear diffraction patterns of cw laser beam at 532 nm passing through a quartz cuvette containing multi-wall carbon nanotubes (MWCNT's) suspended in acetone and in DI water at concentrations of 0.030.wt.%, 0.045 wt.%, 0.060 wt.%, and 0.075 wt.%. Our results show that increasing the concentration of both types of suspensions (MWCNTs in acetone and MWCNTs DI water) led to increase in the number of pattern rings which indicates an increase in their nonlinear refractive indices. Moreover, MWCNTs DI water suspension at a concentration of 0.075 wt. % was more effic

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Publication Date
Sun Apr 15 2018
Journal Name
Strojniški Vestnik - Journal Of Mechanical Engineering
Comparative Experimental and Numerical Investigation on Electrical Discharge Drilling of AISI 304 using Circular and Elliptical Electrodes
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This work introduces a new electrode geometry for making holes with high aspect ratios on AISI 304 using an electrical discharge drilling (EDD) process. In addition to commercially available cylindrical hollow electrodes, an elliptical electrode geometry has been designed, manufactured, and implemented. The principal aim was to improve the removal of debris formed during the erosion process that adversely affects the aspect ratio, dimensional accuracy, and surface integrity. The results were compared and discussed to evaluate the effectiveness of electrode geometry on the machining performance of EDD process with respect to the material removal rate (MRR,) the electrode wear rate (EWR), and the tool wear ratio (TWR). Dimensional features an

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