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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
Thu Jan 25 2024
Journal Name
Biomedical Materials
Enhancing the therapeutic potential of curcumin: a novel nanoformulation for targeted anticancer therapy to colorectal cancer with reduced miR20a and miR21 expression
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Abstract<p>Curcumin (Cur) possesses remarkable pharmacological properties, including cardioprotective, neuroprotective, antimicrobial, and anticancer activities. However, the utilization of Cur in pharmaceuticals faces constraints owing to its inadequate water solubility and limited bioavailability. To overcome these hurdles, there has been notable focus on exploring innovative formulations, with nanobiotechnology emerging as a promising avenue to enhance the therapeutic effectiveness of these complex compounds. We report a novel safe, effective method for improving the incorporation of anticancer curcumin to induce apoptosis by reducing the expression levels of miR20a and miR21. The established</p> ... Show More
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Publication Date
Sun Mar 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
The Influence of x ratio and Annealing Temperatures on Structural and Optical Properties for (CuO)<sub>x</sub>(ZnO)<sub>1-x</sub> Composite Thin Films Prepared by PLD
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Abstract<p>Thin films of (CuO)<sub>x</sub>(ZnO)<sub>1-x</sub> composite were prepared by pulsed laser deposition technique and x ratio of 0≤ x ≤ 0.8 on clean corning glass substrate at room temperatures (RT) and annealed at 373 and 473K. The X-ray diffraction (XRD) analysis indicated that all prepared films have polycrystalline nature and the phase change from ZnO hexagonal wurtzite to CuO monoclinic structure with increasing x ratio. The deposited films were optically characterized by UV-VIS spectroscopy. The optical measurements showed that (CuO)<sub>x</sub>(ZnO)<sub>1-x</sub> films have direct energy gap. The energy band gaps of prepared thin films </p> ... Show More
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Publication Date
Thu Oct 20 2022
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A study of Hepcidin levels and other Biochemical parameters in woman with Osteoporosis with Type 2 Diabetes Mellitus
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Background: Diabetes mellitus (DM) could be regarded as a set of chronic metabolic disorders which have a common aspect of hyperglycemia. The resistance in the peripheral actions of insulin or impaired insulin secretion could be the reason  hepcidin which is a peptide hormone derived from liver, in systemic iron homeostasis is an essential regulator, and its lopsided production participates in the pathogenesis of iron disorders in spectrum. Osteoporosis often accompanies many diseases like ß-thalassemia, hemochromatosis, sickle liver diseases, cell disease and hemosiderosis featured by iron overload, evidences suggest that Iron overload and iron deficiency are suggested by evidences that they affect bone in a negative way, acting

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
factors determining pricing strategies in Iraqi business market – on analytic study in a number of industrial sector companies
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Pricing has an important position among the elements of marketing mixture (4ps) as it represents revenues that in turn represent one of the important  pillars' for resources affecting on organizations sustainability and development , and the failure in determining prices and their strategies has a dangerous effect on the organizations reality and future as a whole . from this point,  this is what from the focus of the research problem,which centered on how to get companies to critical price that satisfies customers and achieve corporate objectives.                          

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Publication Date
Thu Oct 12 2023
Journal Name
Journal Of Pakistan Association Of Dermatologists
Association of Human Herpesvirus Type 8 (HHV-8) expression in patients with Kaposi’s sarcoma: A clinico-immunohistochemical study
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Abstract Background: Kaposi’s sarcoma (KS) is an angioproliferative neoplastic disorder that occurs in different epidemiological forms. Human Herpesvirus type 8 (HHV-8) is established as a causative agent of KS that has been mentioned in textbooks and literature. In the last two decades, KS cases were up searched through many Iraqi medical researches which have been published, but unfortunately, none of which had confirmed this association. Objectives: To assess the association of latent nuclear antigen-1(LANA-1) of HHV-8 among KS patients with clinicopathological parameters and to evaluate if this procedure is valuable for diagnosing this disease through the first immunohistochemical study in Iraq. Methods: This is a clinico-immunohis

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Publication Date
Mon Dec 18 2017
Journal Name
Al-khwarizmi Engineering Journal
Experimental Study of Mixed Convection in an Enclosure with a Cold Movable Top Wall and Hot Bottom Wall
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Mixed convection heat transfer to air inside an enclosure is investigated experimentally. The bottom wall of the enclosure is maintained at higher temperature than that of the top wall which keeps in oscillation motion, whereas the left and right walls are well insulated. The differential temperature of the bottom and top walls changed several times in order to accurately characterize the temperature distribution over a considerable range of Richardson number. Adjustable aspect ratio box was built as a test rig to determine the effects of Richardson number and aspect ratio on the flow behavior of the air inside the enclosure. The flow fields and the average Nusselt number profiles were presented in this wo

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Publication Date
Thu Mar 13 2025
Journal Name
Journal Of Lifestyle And Sdgs Review
Enhancing Sustainability Reporting in Green Universities Through Social Media: A Case Study of Baghdad University on Advancing SDG
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Objectives: This study aims to evaluate the role of social media in promoting awareness of green university initiatives and assess the effectiveness of sustainability reports in engaging students at Baghdad University. In alignment with Sustainable Development Goal 12 (Responsible Consumption and Production),It seeks to provide recommendations for enhancing digital platforms for sustainability communication.   Theoretical Framework: The study is grounded in the Green University Model, Social Media Engagement Theory, and the Sustainability Reporting Framework, which emphasize integrating sustainable practices in education, using digital platforms for community engagement, and leveraging sustainability reports for transparency and

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Publication Date
Sun Aug 31 2014
Journal Name
Arabian Journal Of Geosciences
Petroleum system modeling and risk assessments of Ad’daimah oil field: a case study from Mesan Governorate, south Iraq
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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
Disjuncts and Conjuncts: A Syntactic Type of Study to Evaluate Kurdish Students' Writing in English (At University Level)
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The principal concern of this study is Disjunct and Conjunct adverbials in the
English language. The study sets out to explore and clarify the types, nature and
structure of disjuncts and conjuncts. It also aims at testing student's performance to
evaluate the use and usage of the disjuncts and conjuncts in their written performance.
Two tests, accordingly, were given to some fifty students of at the Dept. of English, at
the college of languages (third and fourth stages) in the University of Sulaimani. The
hypothesis that the study was based on are those students use disjuncts and conjuncts
hardly enough in their writings and when doing so, they generally tend to stick only to
the most commonly used and familiar o

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Publication Date
Sun May 15 2022
Journal Name
Al-kindy College Medical Journal
Assessment of Nurses’ Knowledge, Attitude, and Practices on Antibiotic Use and Resistance in Baghdad: A single-hospital study
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Background: There are so many evidences that there was antimicrobial resistance, and there were many strains that emerged which were difficult to treat. We are living in a situation that the dissemination of multiple drug resistant bacteria can lead us to the situation, in which no treatment could be offered for bacterial infection in future.

Aim of study: Assessment of nurses’ knowledge, attitude, and practices on antibiotic use and resistance in Fatima Al Zahra hospital in Baghdad.

Subjects and Methods:  A cross-sectional study. The study was carried on from 1st of February to 31st of March 2021.  A questionnaire was constructed by the research team based on literature review and was adapted to asses

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