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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
Sat Jun 04 2022
Journal Name
Al–bahith Al–a'alami
The Iraqi public's uses of digital television and cinema sites ( A field study ): Research extracted from a master's thesis
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The research problem revolves around the Iraqi public's use of digital television and cinematic websites، and their importance to the academic study and society، as it examines the public's relationship with these websites، usage habits، and the reasons for their interaction with them. And for the prevalence of this phenomenon of use، it was necessary to address the intensity، intentionality، and timing of use to theoretically root the subject of the study، which is one of the modern studies in Iraq and the Arab world. The survey approach، where the research was based on the theory of uses and gratifications that confer positivity and activity on the mass media audience.

     The researchers designed

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Publication Date
Wed Mar 09 2022
Journal Name
Journal Of Craniofacial Surgery
The Use of Osseodensification for Ridge Expansion and Dental Implant Placement in Narrow Alveolar Ridges: A Prospective Observational Clinical Study
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The osseodensification (OD) drilling technique was suggested as an alveolar ridge expansion technique, so the aim of this prospective clinical study was to evaluate the amount of bone expansion obtained by the OD drilling technique and its effect on implant stability in patients with narrow alveolar ridges. The width of the alveolar ridge was measured at the crest before and after implant site preparation, whereas the implant stability was measured using Osstell Beacon implant stability quotient (ISQ). The ISQ values were recorded immediately postoperatively and after 16 weeks. Twenty-three patients were included; they received 40 implants. The mean (± standard deviation [SD]) amount of expansion was 1.29 (± 0.41) mm, and the difference b

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Publication Date
Mon Feb 01 2021
Journal Name
Iop Conference Series: Materials Science And Engineering
On modelling and adaptive control of a linear smart beam model interacting with fluid
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Abstract<p>This paper deals with modelling and control of Euler-Bernoulli smart beam interacting with a fluid medium. Several distributed piezo-patches (actuators and/or sensors) are bonded on the surface of the target beam. To model the vibrating beam properly, the effect of the piezo-patches and the hydrodynamic loads should be taken into account carefully. The partial differential equation PDE for the target oscillating beam is derived considering the piezo-actuators as input controls. Fluid forces are decomposed into two components: 1) hydrodynamic forces due to the beam oscillations, and 2) external (disturbance) hydrodynamic loads independent of beam motion. Then the PDE is discretized usi</p> ... Show More
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Publication Date
Mon Nov 06 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
Effect of hunting cooperation and fear in a food chain model with intraspecific competition
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Taking into account the significance of food chains in the environment, it demonstrates the interdependence of all living things and has economic implications for people. Hunting cooperation, fear, and intraspecific competition are all included in a food chain model that has been developed and researched. The study tries to comprehend how these elements affect the behavior of species along the food chain. We first examined the suggested model's solution properties before calculating every potential equilibrium point and examining the stability and bifurcation nearby. We have identified the factors that guarantee the global stability of the positive equilibrium point using the geometric approach. Additionally, the circumstances that would gu

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Publication Date
Sun Dec 01 2024
Journal Name
Journal Of Economics And Administrative Sciences
Nadaraya-Watson Estimation of a Circular Regression Model on Peak Systolic Blood Pressure Data
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Purpose: The research aims to estimate models representing phenomena that follow the logic of circular (angular) data, accounting for the 24-hour periodicity in measurement. Theoretical framework: The regression model is developed to account for the periodic nature of the circular scale, considering the periodicity in the dependent variable y, the explanatory variables x, or both. Design/methodology/approach: Two estimation methods were applied: a parametric model, represented by the Simple Circular Regression (SCR) model, and a nonparametric model, represented by the Nadaraya-Watson Circular Regression (NW) model. The analysis used real data from 50 patients at Al-Kindi Teaching Hospital in Baghdad. Findings: The Mean Circular Erro

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Publication Date
Sun Sep 01 2019
Journal Name
Baghdad Science Journal
An Analysis of a Partial Temporary Immunity SIR Epidemic Model with Nonlinear Treatment Rate
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     A partial temporary immunity SIR epidemic model involv nonlinear treatment rate is proposed and studied. The basic reproduction number  is determined. The local and global stability of all equilibria of the model are analyzed. The conditions for occurrence of local bifurcation in the proposed epidemic model are established. Finally, numerical simulation is used to confirm our obtained analytical results and specify the control set of parameters that affect the dynamics of the model.

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Publication Date
Fri May 05 2023
Journal Name
International Journal Of Professional Business Review
The Effect of Emotional Intelligence on Manager Performance: a Field Study in the General Authority for Irrigation and Reclamation Projects in Baghdad
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Purpose: the purpose of this study is to investigate how managers working for the General Authority for Irrigation and Reclamation Projects react to the impact of Emotional Intelligence (EI) on their performance.   Theoretical framework: The current study includes an intellectual framework on two variables, namely EI and Manager Performance (MP), because it is essential to investigate the relationship between these two variables and the impact of EI on MP.   Design/methodology/approach: The research problem is that a manager's capacity to make wise decisions about their work or interactions with subordinates is diminished when they have inadequate EI. The questionnaire is used as a tool for gathering data for the study, and the st

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Publication Date
Thu Sep 08 2022
Journal Name
Al-khwarizmi Engineering Journal
Study of Microbial Desalination Cell Performance; Power Generation and Desalination Efficiency using Pure Oxygen in a Cathode Chamber
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Microbial Desalination Cell (MDC) is capable of desalinating seawater, producing electrical power and treating wastewater. Previously, chemical cathodes were used, which were application restrictions due to operational expenses are quite high, low levels of long-term viability and high toxicity. A pure oxygen cathode was using, external resistance 50 and 150 k Ω were studied with two concentrations of NaCl in the desalination chamber 15-25 g/L which represents the concentration of brackish water and sea water. The highest energy productivity was obtained, which amounted to 44 and 46 mW/m3, and the maximum limit for desalination of saline water was (31% and 26%) for each of 25 g / L and 15 g / L, respectively, when using an ex

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Publication Date
Mon May 04 2020
Journal Name
Environmental Engineering Research
Experimental and modeling study of water defluoridation using waste granular brick in a continuous up-flow fixed bed
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Contamination of surface and groundwater with excessive concentrations of fluoride is of significant health hazard. Adsorption of fluoride onto waste materials of no economic value could be a potential approach for the treatment of fluoride-bearing water. This experimental and modeling study was devoted to investigate for the first the fluoride removal using unmodified waste granular brick (WGB) in a fixed bed running in continuous mode. Characterization of WGB was carried out by FT-IR, SEM, and EDX analysis. The batch mode experiments showed that they were affected by several parameters including contact time, initial pH, and sorbent dosage. The best values of these parameters that provided maximum removal percent (82%) with the in

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Publication Date
Thu Aug 30 2018
Journal Name
Journal Of Engineering
Monitoring Land Cover Change Using Remote Sensing and GIS Techniques: a Case Study of Al-Dalmaj Marsh, Iraq
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Al-Dalmaj marsh and the near surrounding area is a very promising area for energy resources, tourism, agricultural and industrial activities. Over the past century, the Al-Dalmaje marsh and near surroundings area endrous from a number of changes. The current study highlights the spatial and temporal changes detection in land cover for Al-Dalmaj marsh and near surroundings area using different analyses methods the supervised maximum likelihood classification method, the Normalized  Difference Vegetation Index (NDVI), Geographic Information Systems(GIS),  and Remote Sensing (RS). Techniques spectral indices were used in this study to determine the change of wetlands and drylands area and of other land classes, th

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