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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 Dec 01 2021
Journal Name
Baghdad Science Journal
A Prevalence study of Entamoeba spp. in Basrah Province using Different Detection Methods
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This study aims to determine the prevalence of Entamoeba histolytica, Entamoeba dispar and
Entamoeba moshkovskii by three methods of diagnosis (microscopic examination, cultivation and PCR) that
were compared to obtain an accurate diagnosis of Entamoeba spp. during amoebiasis. Total (n=150) stool
samples related to patients were (n = 100) and healthy controls (n= 50). Clinically diagnosed stool samples
(n=100) were collected from patients attending the consultant clinics of different hospitals in Basrah during
the period from January 2018 to January 2019. The results showed that 60% of collected samples were
positive in a direct microscopic examination. All samples were cultivated on different media; the Bra

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Publication Date
Sun Jun 29 2025
Journal Name
Journal Of Physical Education
A comparative analysis , for some Elkinmetekih variables , in the performance of the skill (Nick shot the front reverse ) , between the players of the Iraqi team and the Egyptian , for young people in squash
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Publication Date
Thu Dec 01 2022
Journal Name
Baghdad Science Journal
Molecular Characterization of Potential Crop Pathogens Associated with Weeds as Endophytes in Uniilorin Plantations, Nigeria
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Crop diseases are usually caused by inoculum of pathogens which might exist on alternate hosts or weeds as endophytes. These endophytes, cum pathogens, usually confer some beneficial attributes to these weeds or alternate hosts from protection against herbivores, disease resistance, stress tolerance to secondary metabolites production. This study was therefore carried out to isolate potential crop pathogens which exist as endophytes on weed species in the University of Ilorin plantations. Green asymptomatic leaves were collected from 10 weed species across the plantations, and processed for their endophytic fungi isolation. Isolates were purified into pure cultures and used for molecular identification using the internal transcribed spac

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Publication Date
Thu Mar 11 2021
Journal Name
Annals Of Tropical Medicine & Public Health
Morphological and Molecular Study of Biofilm Formation by Enterobacter cloacae
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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of Tropical Medicine And Public Health
Morphological and Molecular Study of Biofilm Formation by Enterobacter cloacae
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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
Fri Mar 01 2024
Journal Name
Journal Of The College Of Languages (jcl)
Picaresque Elements in Selected English and Iraqi Novels: A Comparative Approach
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The paper attempts to find out the elements of picaresque novel in selected English and Iraqi novels. It studies these elements in Henry Fielding’s Joseph Andrews and Adil Abduljabbar’s Arzal Hamad Al-Salim. The paper is divided into four sections. The first is an introduction to the picaresque novel. It gives a definition, a historical background, and the elements of the genre. The second section studies Fielding’s novel focusing on the elements of this type of novel and how it affects the story itself. The paper follows the novel from the beginning to the end showing these elements. The third is dedicated to Abduljabbar’s novel and how the elements of picaresque genre appear in the novel and play an important role in its developm

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Publication Date
Sat Jun 15 2019
Journal Name
Journal Of Baghdad College Of Dentistry
The accuracy of cone-beam computed tomography in the evaluation of boney support of teeth among patients with a unilateral cleft of lip and palate among IraqiPopulation
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Background: To evaluate the bony supports of the teeth adjacent to the area of cleft in patient with unilateral cleft lip and palate and to compare these measurements with the measurements of the same teeth in non-cleft side by using CBCT. Materials and methods: The CBCT scans of 30 patients having cleft lip( unilateral) and palate(unilateral), were analyzed and the measurements of the alveolar bony support for teeth that are adjacent to the cleft area were measured with those teeth located on opposite side (non- clef) side. For each tooth, the measurements will taken for the distance between the( cementoenamel junction) (CEJ) and the bony crest (AC) at the( buccal area) was measured and the thickness of the buccal plate At zero, one, tw

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Publication Date
Wed Feb 01 2023
Journal Name
Colloid Journal
Application of Hydrophilic Lipophilic Difference Theory for Fenofibrate Formulation as a Self-Emulsifying Drug Delivery System
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Improved oral bioavailability of lipophilic substances can be achieved using self-emulsifying drug delivery systems. However, because the properties of self-emulsifying are greatly influenced by surfactant amount and type, type of oil used, droplet size, charge, cosolvents, and physiological variables, the synthesis of self-emulsifying is highly complex; consequently, only a small number of excipient self-emulsifying formulations has been developed so far for clinical use. This study reports a highly effective procedure for developing self-emulsifying formulations using a novel approach based on the hydrophilic-lipophilic difference theory. Microemulsion characteristics, such as the constituents and amounts of oil and surfactant electrolyte

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