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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 Nov 01 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Preparation and characterization of Posaconazole as a Nano-micelles using d-α-Tocopheryl polyethylene glycol 1000 succinate (TPGS)
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It is important to note that Posaconazole (POCZ) is a newly developed extended-spectrum triazole that belongs to BCS class II and has a solubility of less than 1µg/ml. In patients with a weakened immune system, POCZ has been shown to be effective as an antifungal treatment for invasive infections caused by candida and aspergillus species. The nano-micelles technique can be used to increase POCZ solubility. In order to increase their apparent solubility in water, nano-micelles are made by combining macromolecules that self-assemble into ordered structures capable of entrapping hydrophobic drug molecules in the interior domain. Dispersed colloidal systems, of which nano-micelles are a subset, are a large and diverse group. Composed of a p

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Publication Date
Wed Feb 01 2023
Journal Name
Journal Of Engineering
Checking the Accuracy of Selected Formulae for both Clear Water and Live Bed Bridge Scour
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Due to severe scouring, many bridges failed worldwide. Therefore, the safety of the existing bridge (after contrition) mainly depends on the continuous monitoring of local scour at the substructure. However, the bridge's safety before construction mainly depends on the consideration of local scour estimation at the bridge substructure. Estimating the local scour at the bridge piers is usually done using the available formulae. Almost all the formulae used in estimating local scour at the bridge piers were derived from laboratory data. It is essential to test the performance of proposed local scour formulae using field data. In this study, the performance of selected bridge scours estimation formulae was validated and sta

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Publication Date
Sun Mar 06 2022
Journal Name
Al–bahith Al–a'alami
DEPENDENCE OF MEDIA OFFICES ON THE CABINET'S WEBSITE AS A SOURCE OF INFORMATION
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     The research aimed to identify the extent to which the media offices in the ministries depend on the website of the Iraqi Council of Ministers as a source of information. Such goal includes a set of sub-goals: Knowing the reasons for media offices' reliance on the information provided by the Cabinet's website; and revealing the benefit derived from relying on the Cabinet's website.

The researcher used the survey method to screen and comprehend the extent to which the media offices in the ministries depend on the website of the Iraqi Council of Ministers as a source of information.

The mechanism of comprehensive account of the limits of research wa

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Publication Date
Sun Oct 15 2023
Journal Name
Bionatura
Nesfatin-1 is a biomarker that plays a role in the inflammatory process of coronary artery diseases in Iraqi patients with non-alcoholic fatty liver disease.
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Amis: NAFLD is considered to be the most common cause of liver conditions worldwide. Also, it is a primary reason that leads to coronary artery diseases, limiting blood flow to the heart. Therefore, This study aimed to evaluate the serum level of Nesfatin-1 and its ability to indicate the prognosis of CAD in patients with NAFLD. Material & Methods: one-hundred eighty Individuals were enrolled in the study, including In both genders, blood was collected from each Individual and sent to the laboratory for biochemical tests. Findings: Data from the current study showed a significant increase in Nesfatin-1 in the CAD group and a significant decrease in Nesfatin-1 in the NAFLD group compared to the control group. In addition, there w

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Publication Date
Sun Dec 30 2012
Journal Name
College Of Islamic Sciences
A study of the hadiths of supplication orchestration
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A study of the hadiths of supplication orchestration

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Publication Date
Tue Oct 02 2018
Journal Name
Iraqi Journal Of Physics
Informative accuracy investigation and updating map using remote sensing technique and GIS
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In this work, using GPS which has best accuracy that can be established set of GCPs, also two satellite images can be used, first with high resolution QuickBird, and second has low resolution Landsat image and topographic maps with 1:100,000 and 1:250,000 scales. The implementing of these factors (GPS, two satellite images, different scales for topographic maps, and set of GCPs) can be applying. In this study, must be divided this work into two parts geometric accuracy and informative accuracy investigation. The first part is showing geometric correction for two satellite images and maps.
The second part of the results is to demonstrate the features (how the features appearance) of topographic map or pictorial map (image map), Where i

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Publication Date
Sat Aug 01 2020
Journal Name
Key Engineering Materials
Compressive Strength Performance of Reactive Powder Concrete Using Different Types of Materials as a Partial Replacement of Fine Aggregate
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Reactive Powder Concrete (RPC) can be incorporate as a one of the most important and progressive concrete technology. It is a special type of ultra-high strength concrete (UHSC) that’s exclude the coarse aggregate from its constitutive materials. In this research an experimental study had been carried out to investigate the effect of using three types of materials (porcelain aggregate) and others sustainable materials (glass waste and granular activated carbon) as a partial replacement of fine aggregate. Four percentages had considered (0, 10, 15 and 20) % to achieve better understanding for the influence of these materials upon the compressive strength of RPC. Four curing ages had included in this study, these are; 7, 28, 60 and

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Publication Date
Sat Aug 01 2020
Journal Name
Key Engineering Materials
Compressive Strength Performance of Reactive Powder Concrete Using Different Types of Materials as a Partial Replacement of Fine Aggregate
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Reactive Powder Concrete (RPC) can be incorporate as a one of the most important and progressive concrete technology. It is a special type of ultra-high strength concrete (UHSC) that’s exclude the coarse aggregate from its constitutive materials. In this research an experimental study had been carried out to investigate the effect of using three types of materials (porcelain aggregate) and others sustainable materials (glass waste and granular activated carbon) as a partial replacement of fine aggregate. Four percentages had considered (0, 10, 15 and 20) % to achieve better understanding for the influence of these materials upon the compressive strength of RPC. Four curing ages had included in this study, these are; 7, 28, 60 and

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Production of fibrinolytic protease from various fungal isolates and species 2.Determination of optimum conditions for enzyme production from Pleurotus ostreatus
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The optimum conditions for production of fibrinolytic protease from an edible mushroom Pleurotus ostreatus grown on the solid medium , Sus medium, composed of Sus wastes (produced from extracted medicinal plant Glycyrrhiza glabra) were determined. Addition of 5% of Soya bean seeds meal in Sus medium recorded a maximum fibrinolytic protease activity resulting in 7.7 units / ml. The optimum moisture content of Sus medium supplemented with 5% Soya bean seeds meal was 60% resulting in 7.2 units / ml.Pleurotus ostreatus produced a maximum fibrinolytic protease activity when the spawn rate,pH of medium and incubation temperature were 2,6 and 30°C, respectively. The maximum fibrinolytic protease activity was 7.6 units / ml when incubat

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
A study of some atomic properties for He-like selected ions
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The atomic properties have been studied for He-like ions (He atom, Li+, Be2+ and B3+ions). These properties included, the atomic form factor f(S), electron density at the nucleus , nuclear magnetic shielding constant and diamagnetic susceptibility ,which are very important in the study of physical properties of the atoms and ions. For these purpose two types of the wave functions applied are used, the Hartree-Fock (HF) waves function (uncorrelated) and the Configuration interaction (CI) wave function (correlated). All the results and the behaviors obtained in this work have been discussed, interpreted and compared with those previously obtained.

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