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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
Mon Dec 01 2025
Journal Name
International Communications In Heat And Mass Transfer
Design optimization and performance analysis of a PCM-to-air heat exchanger with optimized fin configuration for building heating applications
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Publication Date
Thu Nov 02 2023
Journal Name
Journal Of Engineering
Optimum Reinforcement Depth Ratio for Sandy Soil Enhancement to Support Ring Footing Subjected to a Combination of Inclined-Eccentric Load
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This work investigates the impacts of eccentric-inclined load on ring footing performance resting on treated and untreated weak sandy soil, and due to the reduction in the footing carrying capacity due to the combinations of eccentrically-inclined load, the geogrid was used as reinforcement material. Ring radius ratio and reinforcement depth ratio parameters were investigated. Test outcomes showed that the carrying capacity of the footing decreases with the increment in the eccentric-inclined load and footing radius ratio. Furthermore, footing tilt and horizontal displacement increase with increasing the eccentricity and inclination angle, respectively. At the same time, the increment in the horizontal displacement due t

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Publication Date
Wed Sep 29 2021
Journal Name
College Of Islamic Sciences
The position of Al-Jassas (D. 370 AH) of the verses of "As-Sifat Al-Khbriya"
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This research aims at know the position of Al-Jassas Al- Hanafi (D. 370 AH) of  "As-Sifat Al- Khbriya", through his interpretation: (the provisions of Qur'an), by studying his interpretation of the verses related to this issue.

The most significant results of this study that Al-Jassas did not consider the words that called: "As-Sifat Al- Khbriya" as adjectives to Allah almighty, but he consider them contained an inappropriate meaning to Allah almighty, thus it must be referred to the perfect arbitrator, so he was believe in opinion of interpretation. and interpretations of Al-Jassas for the related of the Qur'an verses relat

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Publication Date
Fri Sep 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Choosing the best method for estimating the survival function of inverse Gompertz distribution by using Integral mean squares error (IMSE)
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In this research , we study the inverse Gompertz distribution (IG) and estimate the  survival function of the distribution , and the survival function was evaluated using three methods (the Maximum likelihood, least squares, and percentiles estimators) and choosing the best method estimation ,as it was found that the best method for estimating the survival function is the squares-least method because it has the lowest IMSE and for all sample sizes

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Publication Date
Fri Dec 30 2022
Journal Name
Voprosy Istorii
Changing the agricultural map of Diyala Governorate for the years (1980, 1990, 2000, 2010, 2020) using GIS and remote sensing
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Abstract. Geographical and remote sensing, which gave a picture of the change in the area of agricultural land in the study area for selected years (1980, 1990, 2000, 2010, 2020). In particular and Iraq in general, as this led to a reduction in the areas of agricultural lands and in return an increase in arid lands and their desertifica- tion and the loss of their productive value, which as a result leads to the migration of the population, the change of land sex, the failure to achieve food security and dependence on the import of the food basket.

Publication Date
Fri Sep 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Choosing the best method for estimating the survival function of inverse Gompertz distribution by using Integral mean squares error (IMSE)
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In this research , we study the inverse Gompertz distribution (IG) and estimate the  survival function of the distribution , and the survival function was evaluated using three methods (the Maximum likelihood, least squares, and percentiles estimators) and choosing the best method estimation ,as it was found that the best method for estimating the survival function is the squares-least method because it has the lowest IMSE and for all sample sizes

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Publication Date
Fri Sep 16 2022
Journal Name
Asian Journal Of Water, Environment And Pollution
Comparative of Green-Synthesis of Bimetallic Nanoparticles Iron/Nickel (Fe/Ni) and Supported on Zeolite 5A: Heterogeneous Fenton-like For Dye Removal From Aqueous Solutions
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Green synthesis of bimetallic nanoparticles of Fe/Ni (G-Fe/Ni-NPs) and zeolite-5A supported (G-Z-Fe/Ni-NPs) as heterogeneous Fenton-like oxidation for the decolourisation of reactive red 120-dye (RR120) from the aqueous medium using green tea extract as a reducing agent. Zeolite-5A from local kaolin is prepared and characterised using the hydrothermal method and is used as a supporting material for Fe/Ni-NPs. (SEM), (EDX), (AFM), (XRD), (FT-IR), (BET). Its zeta potential were used to characterise G-Fe/Ni-NPs and G-Z-Fe/Ni-NPs. The decolourisation efficiency (Ed) of the RR120-dye using a heterogeneous Fenton-like for G-Fe/Ni-NPs and G-Z-Fe/Ni-NPs is 99.8% and 99.9%, respectively, under the optimum conditions: [H2O2] = 20 and 1 mmol/L

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Publication Date
Fri Mar 11 2016
Journal Name
International Journal Of Applied Linguistics And English Literature
The Illusion of Untranslatability: A Theoretical Perspective with Reference to the Translation of Culture-Bound Euphemistic Expressions in the Qur'an
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The present study investigates the notion of untranslatability where the concept of equivalence is reconsidered since the misconceptions, related to the said concept, inevitably lead to the emergence of untranslatability. Identifying equivalence as relative, approximate and necessary identity makes the notion of untranslatability a mere theorization. The objectives of the present study are (1) to investigate the notion of untranslatability in terms of the misconceptions associated with the concept of equivalence (2) to examine the possibility of translatability from Arabic into English focusing on culture-bound euphemistic expressions in the Quran as an area of challenge in translation. Data on the translation of culture-bound euphemistic e

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Publication Date
Wed Apr 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
A specimen of the internal control system on the stock in light of the application JIT system In construction companies
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Suffer most of the facilities of the high cost of inventory , which affects the high cost of the product and thus affects many administrative decisions , as well as suffer the facilities of the systems developed by the provisions of inventory control , and this problem is exacerbated in the construction sector where the inventory in the form of Construction spin of the Year for another it becomes difficult to control the cost effectively , and is the research problem in question follows: What are the implications of the use of the system in time inventory accounting system for the contracting company does kills Alrkaah to the provisions of the cost of inventory and what is the optimal approach to inventory control ? Find assumed

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Publication Date
Sun Jan 01 2023
Journal Name
2nd International Conference On Mathematical Techniques And Applications: Icmta2021
Polynomial image compression: A review
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