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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
Wed May 26 2021
Journal Name
Communications In Mathematical Biology And Neuroscience
Modelling and stability analysis of the competitional ecological model with harvesting
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The interplay of predation, competition between species and harvesting is one of the most critical aspects of the environment. This paper involves exploring the dynamics of four species' interactions. The system includes two competitive prey and two predators; the first prey is preyed on by the first predator, with the former representing an additional food source for the latter. While the second prey is not exposed to predation but rather is exposed to the harvest. The existence of possible equilibria is found. Conditions of local and global stability for the equilibria are derived. To corroborate our findings, we constructed time series to illustrate the existence and the stability of equilibria numerically by varying the different values

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Publication Date
Mon Jun 20 2022
Journal Name
International Journal Of Early Childhood Special Education
The Impact of the Visual Teaching Strategy by using Infographic in mathematics achievement for intrmediate grade students
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The research aims to identify the impact of the visual teaching strategy by using infographics mathematics achievement for intermediate grade students. The experimental research method was adopted, as the experimental design of two independent and equal groups with a post test was used, whereas the experiment was applied on a sample consisting of (52) male students from first- intermediate grade students in (Al-Haq Al-Mubin intermediate school for Boys) of the General Directorate in Anbar Governorate - Department Education in Fallujah for the academic year (2021-2022), and the research sample was distributed equally on the two research groups, and Division (B) was chosen randomly to be the experimental group, while Division (A) was the cont

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Publication Date
Sun Apr 06 2014
Journal Name
Journal Of Economics And Administrative Sciences
Modeling Absolute Deviations Method by using Numerical Methods to measure the dispersion of the proposal for error
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Is in this research review of the way minimum absolute deviations values ​​based on linear programming method to estimate the parameters of simple linear regression model and give an overview of this model. We were modeling method deviations of the absolute values ​​proposed using a scale of dispersion and composition of a simple linear regression model based on the proposed measure. Object of the work is to find the capabilities of not affected by abnormal values by using numerical method and at the lowest possible recurrence.

 

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Publication Date
Mon Aug 18 2025
Journal Name
Soil And Sediment Contamination: An International Journal
Remediation Prediction of Contaminated Soil with Crude Oil Using the Optimized Remediation Method for the Iraqi Environment
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Large quantities of petroleum-contaminated soil are generated with increased global energy consumption and crude oil production. This theoretical study evaluates the treatment of 1 ton of petroleum-contaminated soil using seven methods: incineration, physical washing, chemical washing, thermal pyrolysis, Fenton-oxidation-pyrolysis, the biological treatment, and asphaltenes. Data were based on experimental results from the Nahran Bin Omar oil lake in Basra Governorate, Iraq, (2019–2021). The methods were compared by waste generation, treatment cost, and duration. Results indicate that using petroleum-contaminated soil as a raw material for asphalt manufacturing is most beneficial since it is sold as a raw material. Incineration is faster a

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Publication Date
Wed Feb 20 2019
Journal Name
Iraqi Journal Of Physics
The measurements of neutron Fermi Age for selected Nuclear Reactor shielding materials using the Indium foil technique
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The Neutron Fermi Age, t, and the neutron slowing down density,   q (r, t) , have been measured for some materials such as Graphite and Iron by using gamma spectrometry system UCS-30 with NaI (Tl) detector. This technique was applied for Graphite and Iron materials by using Indium foils covered by Cadmium and the measurements done at the Indium resonance of 1.46 eV. These materials are exposed to a plane 241Am/Be neutron source with recent activity 38 mCi. The measurements of the Fermi Age were found to be t = 297 ± 21 cm2 for Graphite, t = 400 ± 28 cm2 for Iron. Neutron slowing down density was also calculated depending on the recent experimental t value and distance.

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Publication Date
Fri Jan 11 2019
Journal Name
Iraqi Journal Of Physics
Study of starch, sugar blending effect on the biodegradability of (PVA) for packaging applications
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PVA, Starch/PVA, and Starch/PVA/sugar samples of different
concentrations (10, 20, 30 and 40 % wt/wt) were prepared by casting
method. DSC analysis was carried; the results showed only one glass
transition temperature (Tg) for the samples involved, which suggest
that starch/PVA and starch/PVA/sugar blends are miscible. The
miscibility is attributed to the hydrogen bonds between PVA and
starch. This is in a good agreement with (FTIR) results. Tg and Tm
decrease with starch and sugar content compared with that for
(PVA). Systematic decrease in ultimate strength, due to starch and
sugar ratio increase, is attributed to (PVA), which has more hydroxyl
groups that made its ultimate strength higher than that for

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Publication Date
Wed Jul 01 2026
Journal Name
Journal Of Materials In Civil Engineering
Interlaboratory Study on the Use of Sugarcane Molasses for Production of Bioasphalt: Field Application
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The growing demand for sustainable and environmentally friendly alternatives in road construction has led to the exploration of bio-based materials for bitumen modification. This study investigates the use of sugarcane molasses (SM) as a partial replacement of bitumen, evaluating its performance through an interlaboratory study conducted in India and Iraq. Bio-bitumen binders were prepared by partially replacing 30% of conventional bitumen with sugarcane molasses, and their chemical and thermal behaviour was studied. Additionally, laboratory tests were conducted on bio-bitumen mixtures, evaluating rutting resistance, cracking resistance, moisture susceptibility, and stiffness characteristics. A mechanistic-empirical pavement analysis using

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Publication Date
Fri Aug 27 2021
Journal Name
Journal Of Craniofacial Surgery
The Effects of Local Alendronate With or Without Recombinant Human Bone Morphogenetic Protein 2 on Dental Implant Stability and Marginal Bone Level: A Randomized Controlled Study
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The aim of this study was to evaluate the effects of local application of bisphosphonate gel and recombinant human bone morphogenic protein 2 gel, on titanium dental implant stability and marginal bone level. Twenty-seven patients with upper and lower missing posterior tooth/teeth were included in the study with a total of 71 implants that were used for rehabilitation. The implants were randomly divided into 4 groups: 3 study groups and 1 control. Group1; local application of bisphosphonate gel, group 2; local application of recombinant human bone morphogenic protein 2 gel, group 3; local application of a mixed formula of both gels. The gel application was immediately preimplant insertion, group 4; implant insertion without application of a

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Publication Date
Mon Jul 29 2019
Journal Name
International Journal Of Energy Research
Performance of the dye‐sensitized solar cells fabricated using natural dyes from <i>Ixora coccinea</i> flowers and <i>Cymbopogon schoenanthus</i> leaves as sensitizers
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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
A political perusal of Initiations in Declaring Middle East a District vacant of mass Destruction weapons
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A political perusal of Initiations in Declaring Middle East a District vacant of mass Destruction weapons

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