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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 Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
Comparison Between the Methods Estimate Nonparametric and Semiparametric Transfer Function Model in Time Series Using Simulation
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Publication Date
Fri Jan 19 2024
Journal Name
Research Journal Of Pharmacy And Technology
Serum Levels of Fetuin-A, Ischemia-modified Albumin (IMA), and Ferritin in Hospitalized patients with severe COVID-19. A Case-control Study
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Objective: To measure the serum levels of Fetuin-A, ischemia-modified albumin (IMA), and ferritin in hospitalized patients with severe COVID-19in Baghdad, Iraq. Moreover, to determine these biomarkers' cut-off valuesthat differentiate between severely ill patients and control subjects. Methods: This case-control study was done from 15 September to the end of December 2021 and involved a review of the files and collectionof blood samples from patients (n=45, group1) hospitalized in COVID-19 treatment centersbecause of severe symptoms compared tohealthy subjects as controls (n=44, group2). Results: Fetuin-A serum levels were not statistically different between patients and controls. In contrast, IMA and ferritin levels were significan

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Publication Date
Thu Nov 19 2020
Journal Name
The Iraqi Journal For Information And Documentation Studies
The use of still and animated comics in providing user services in university information institutions: a field study
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Comics is a visual art (Still and motion pictures) it seeks to provide a Training courses are a series of intensive important educational and complementary programs, based on previous foundation experiences. Create to development the participants in aspects of specialization according to the requirements of the educational system to continue developing the previous scienti􀂡c and practical experiences. Personally, or adopted by the trainee institution, where the trainee gets a professional skill certi􀂡cate that contributes to the development his work.Development and Continuous Education Center (DCEC) at the University of Baghdad (UoBaghdad) is a center dedicated to continuing education courses in which the participant is awarded a cert

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Modes of Knowledge acquisition and their reflections on the tacit knowledge A field study in Tuz General Hospital
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This research aims to knowledge the extent of the application of Tuz General Hospital to the concept of tacit knowledge dimensions (mental models, intuition, experience, skill) and methods of acquiring knowledge dimensions (training, job rotation, work teams) and the measurement and analysis of the link and the kind of impact between the methods of acquiring knowledge and tacit knowledge of the Angels nursing in the researched hospital, and was the questionnaire primary means of collecting information adopted by the researcher that, the research sample of (90) individuals, including the Angels nursing, has been using the statistical program spss for the purpose of conducting statistical treatments, and through the diagnosis and m

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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
A Study on the Stability of Different Frusemide Liquid Dosage Formulas: Oral Solution, Syrup, Elixir, Suspension and Emulsion
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The present study aim at preparing frusemide in liquid form suitable for oral use. This is achieved through preparing different liquid forms of frusemide. The frusemide liquid is prepared in the following forms: oral solution, syrup and elixir with intensity of 1, 0.4 and 0.8% weight /volume respectively and in combination with potassium carbonate, polysorbate 80, alcohol and phosphate buffer solution of pH8 to dissolve the frusemide in the above mentioned forms. The different forms of the prepared medicine have been stored in glass bottles that can provide protection against light and at 40, 50, 600C for four months. Besides the pH has been checked to decide the period of validity. The results show that the expiration date of

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Publication Date
Tue Feb 17 2026
Journal Name
Kufa Journal Of Arts
Compound thought :Or face crises from oneself to politics A Philosophical Study on the Editions of Edgar Moran
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Publication Date
Sun Dec 01 2019
Journal Name
Al-adab Journal
Lamenting the Father in Modern American Poetry: A Study in Selected Elegies of Mark Strand and Sharon Olds
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Modern American elegy reveals a change in the attitude of mourning from the traditional lamenting approach to some antielegiac attitudes towards the mourned figure. Many American poets have lamented the pass away of the stately figure of the father. However, some poets attack their dead father, and ridiculed him in a poem that is intended to be an elegy, instead of showing passion, homage and love to him. In this regard, two poetic attitudes to the father can be traced in modern American poetry. The first one takes the form of tributes and praise, offering great admiration, compassion, and love for the father. For these poets, a father is an inspiration. The second voice develops some anger and contempt against the patriarchal authority emb

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Publication Date
Sun Sep 04 2016
Journal Name
Baghdad Science Journal
A Study the Effect of TiO2 Nanoparticles Combination with Antibiotics and Plant extracts Against Some Gram Negative Bacteria
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Titanium dioxide TiO2 has been widely utilized in cleaning and sterilizing material for many clinical tools sanitary ware, food tableware and cooking and items for use in hospitals. Titanium dioxide TiO2 non toxicity and long term physical and chemical stability. It has been widely used decomposition of organic compounds and microbial organisms such as cancer cell, viruses and bacteria as well as its potential application in sterilization of medical devices. The aim of the study the effect of titanium dioxide TiO2 on some Gram negative bacteria and study their effects on some virulence factors and chromosomal DNA.In this study, we obtained (E. coli ? Proteus mirabilis, Proteus vulgaris ? Pseudomonas aeruginosa ? Klebsiella pneumonia and Ac

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Publication Date
Mon Sep 01 2025
Journal Name
Journal Of Engineering
Petrophysical Evaluation by Integrating AI and HFU Methods. A Case Study of the Mishrif Reservoir in Southern Iraq
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Reservoir quality assessment is important for detecting hydrocarbon-bearing zones and guiding future enhancement strategies. This study presents a detailed petrophysical evaluation of the Mishrif Formation in the Buzurgan Oilfield, which was selected due to its strategic value through its significant remaining reserves which making it an ideal candidate for advanced evaluation techniques. This study aims for shale content, porosity, permeability, water saturation, net to gross, and lithology determination. Well log and core data were used together to establish accurate property estimations. Permeability prediction through conventional methods, like core permeability-porosity correlations, was highly dispersive due to the heterogenei

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Publication Date
Sun Jan 01 2023
Journal Name
The Egyptian Journal Of Hospital Medicine
A Study of the Relation between Human Cytomegalovirus and IL-35 in Rheumatoid Arthritis Disease Patients in Iraq
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ackground An autoimmune and inflammatory illness called rheumatoid arthritis (RA) occurs when your immune system mistakenly attacks normal cells in your body. Interleukin-35 is a brand-new cytokine that belongs to the immunosuppressive and anti-inflammatory IL-12 family. β -herpesvirus that produces inflammation and stays dormant in its host for life is the human cytomegalovirus. Human herpesvirus (HCMV) has been at the core of several RA-related theories. Objective The current study looked at the association between RA and serum IL-35 levels as well as the association between RA and CMV. Patients and methods Blood samples were taken in the Baghdad Teaching Hospital and Typical Rheumatology Unit from January 2022 to Mars 2022 for the curre

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