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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 Nov 01 2025
Journal Name
Construction And Building Materials
Polyalphaolefin as a potential modifying agent for hard asphalt cement: Physical, rheological, and chemical characterization
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Hard-grade asphalt binders like AC20-30 typically exhibit excessive stiffness, reduced penetration, and compromised workability, necessitating modification before use in paving applications. This study evaluates the efficacy of regular polyalphaolefin (PAO), a synthetic olefin-based lubricant, as a performance-enhancing modifying agent for such binders. AC20-30 was blended with PAO at dosages ranging from 2 wt.% to 10 wt.%, and the modified binders were characterized via penetration, ductility, softening point, and rotational viscosity measurements, alongside advanced rheological and chemical-morphological analyses. Incorporating PAO in AC20-30 asphalt progressively reduced the binder stiffness and enhanced its flexibility, with all modifie

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Publication Date
Mon Aug 17 2020
Journal Name
Biochemical And Cellular Archives
SERUM FERRITIN AS A BIOMARKER FOR THYROID GLAND (HYPO AND HYPER) THYRODISM WITH METABOLIC SYNDROME
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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Are obese women potential for inflammatory process? A pilot study
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This study was designed to look for certain biochemical markers(serum uric acid and serum peroxynitrite) in women presented with obesity and to compare the level of these markers with non-obese women. A total number of 63 women were recruited from outpatients and private clinics to admit in this study. The patients were grouped into non obese women (Group I) and obese women (Group II). The anthropometric and blood pressure were determined and venous blood was obtained from each patient for determination of C-reactive protein, uric acid and peroxynitrite. The results showed that there were no significant differences in age or in concomitant or associated diseases in both groups except rheumatoid arthritis which account 80% of group I and 25%

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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of The College Of Languages (jcl)
The Existential Dilemma as a Philosophical Problem in The Beggar by Naguib Mahfouz
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     The Beggar (1965) is a story of isolation and depression which is written by the Egyptian novelist Naguib Mahfouz who is considered the father of Arabic Literature in the modern era. Specifically, he refers in his great novel called The Beggar that the man unable to achieve psychological revival after Nasser’s revolution, the man sacrificed his own job and his family for a desire that increases his feelings of alienation and depression which leads him to an emotional outcry against the indifferent. The main aim of the study highlights the concept of existential dilemma as a philosophical problem and personality crisis by the protagonist of The Beggar novel, Omer Al-Hamzawi who had acc

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Publication Date
Thu Aug 08 2019
Journal Name
Iop Conference Series: Materials Science And Engineering
A Study of poly4-oxo-4-(4-sulfamoylphenylamino) but-2-enoic acid as a good anti – Corrosion of 316L stainless steel in 0.2M hydrochloric acid solution.
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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Comparative study for Environmental Impact Assessment in Environmental Iraqi and Saudi legislation
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Abstract<p>Countries are developing the spatial development of their societies through the projects that they undertake in various ways, and this development may be cause great impact on the environment, which also depend on the type of development, whether industrial, agricultural, or service and after the problems that occurred as a result of development on the environment, most of the countries currently did to legislating laws Environmental and some other procedures before granting environmental approvals for the purpose of establishing spatial development projects. One of the most important of these laws and regulations is Environmental impact assessment (EIA). The environmental impact asse</p> ... Show More
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Publication Date
Thu Jan 24 2019
Journal Name
Journal Of Education College Wasit University
“They’ve damaged your uniqueness”: Technology as a Source of Dystopia in Caryl Churchill’s A Number
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This study focuses on the impact of technology on creating a dystopian world as presented by the English playwright Caryl Churchill in her play A Number (2002). This dramatic work came as a reaction to the most crucial and valuable turning point in the scientific achievements of human engineering, namely, the cloning of the sheep called Dolly. Therefore, A Number is a play that presents an analytical stage for imagining the biotechnological and scientific future. This dramatic vignette captures the playwright’s fears towards the abnormal progress of technology and science and how far such technological progress affects human relationships and identity. It also portrays how technological progress results in the feeling of a lack of

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Publication Date
Tue Jun 01 2021
Journal Name
International Journal Of Nonlinear Analysis And Applications
Bayes estimators of a multivariate generalized hyperbolic partial regression model
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Publication Date
Wed Jan 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Numerical Investigation of Drag Reduction Techniques in a Car Model
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Abstract<p>Reducing the drag force has become one of the most important concerns in the automotive industry. This study concentrated on reducing drag through use of some external modifications of passive flow control, such as vortex generators, rear under body diffuser slices and a rear wing spoiler. The study was performed at inlet velocity (V=10,20,30,40 m/s) which correspond to an incompressible car model length Reynolds numbers (Re=2.62×10<sup>5</sup>, 5.23×10<sup>5</sup>, 7.85×10<sup>5</sup> and 10.46×10<sup>5</sup>), respectively and we studied their effect on the drag force. We also present a theoretical study finite volume method (FVM) of solvi</p> ... Show More
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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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