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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
Sun Jan 01 2017
Journal Name
Al–bahith Al–a'alami
Advertises of Advertising Mail Post of Emirate of Dubai as a sample
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                The advertising mail is considered as one of potential tools that followed to transfer the printed messages to the consumers and public customers whom are located at homes or works. This type of advertising is preferable due to the zero expense to receive the announcements of products, which became recently one of the successful procedures to create new customers and keep them in touch with direct communication. It is also possible to send them to specific group of people who can be classified by the advertisers to select even by name their own clients to give the personality to the clients for a long term of communication.

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Publication Date
Fri Dec 01 2023
Journal Name
Baghdad Science Journal
Numerical Investigation of Physical Parameters in Cardiac Vessels as a New Medical Support Science for Complex Blood Flow Characteristics
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This study proposes a mathematical approach and numerical experiment for a simple solution of cardiac blood flow to the heart's blood vessels. A mathematical model of human blood flow through arterial branches was studied and calculated using the Navier-Stokes partial differential equation with finite element analysis (FEA) approach. Furthermore, FEA is applied to the steady flow of two-dimensional viscous liquids through different geometries. The validity of the computational method is determined by comparing numerical experiments with the results of the analysis of different functions. Numerical analysis showed that the highest blood flow velocity of 1.22 cm/s occurred in the center of the vessel which tends to be laminar and is influe

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Publication Date
Sun Jun 07 2015
Journal Name
Baghdad Science Journal
Serum Vascular Endothelial Growth Factor VEGF and Interlukin-8 As a Novel Biomarkers For Early Detection of Ovarian Tumors
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Epithelial ovarian cancer is the leading cause of cancer deaths from gynecological malignancies. Angiogenesis is considered essential for tumor growth and the development of metastases. VEGF and IL?8 are potent angiostimulatory molecules and their expression has been demonstrated in many solid tumors, including ovarian cancer.VEGF and IL-8 concentrations were measured by ELISA test (HumanVEGF,IL-8). Bioassay ELISA/ US Biological / USA).The median VEGF and IL-8 levels were significantly higher in the sera of ovarian cancer patients than in those with benign tumors and in healthy controls.Pretreatment VEGF and IL-8 serum levels might be regarded as an additional tool in the differentiation of ovarian tumors.

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Publication Date
Tue Jun 20 2023
Journal Name
Baghdad Science Journal
Assessment of image quality of cervical spine complications using Three Magnetic Resonance Imaging Sequences
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Examining and comparing the image quality of degenerative cervical spine diseases through the application of three MRI sequences; the Two-Dimension T2 Weighed Turbo Spin Echo (2D T2W TSE), the Three-Dimension T2 Weighted Turbo Spin Echo (3D T2W TSE), and the T2 Turbo Field Echo (T2_TFE). Thirty-three patients who were diagnosed as having degenerative cervical spine diseases were involved in this study. Their age range was 40-60 years old. The images were produced via a 1.5 Tesla MRI device using (2D T2W TSE, 3D T2W TSE, and T2_TFE) sequences in the sagittal plane. The image quality was examined by objective and subjective assessments. The MRI image characteristics of the cervical spines (C4-C5, C5-C6, C6-C7) showed significant difference

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Local wheat peel as a solid surface to remove Azure B dye from aqueous solution:Equilibrium isotherms and thermodynamic study
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In this research local wheat peel was used as an adsorbent surface for removal of Azure B (AB) dye from the aqueous solution. The adsorption process was performed at different experimental parameters, equilibrium time, temperature, ionic strength and solution pH. The isotherms of adsorption are of H-type as compared with Giles curves and the adsorption data were coincide with Freundlich equation. The adsorption kinetic data were analyzed using pseudo- first and second order kinetic models. The effect of temperature was studied and the amount of dye adsorbed was found to increase with the increasing of temperature from 25 to 50 oC. The values of thermodynamic functions like enthalpy and entropy have been estimated. The quantity of adso

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Publication Date
Mon Sep 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Suggested Model for accounting disclosure proactive and reflect on the decisions of investors: Applied research in a sample of industrial companies listed on the Iraq Stock Exchange
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Often requires the investor to know the result of the company's activity contribute to the investor or by wanting to invest in them because profit or loss of the company affect positively or negatively in the price of shares of the company and with the end of the fiscal year delayed companies often to issue its financial statements after it is approved and audited by an observer External Auditor, From here came the idea of ​​research that appears to stakeholders of financial statements proactive appear, including actual figures for earlier stages have been prepared lists about lists and planned by the administration reflect the results of its phase remainder of the year as if they are (half a year or season or month) to offer At the

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
The regulatory climate in the government and private kindergarten children (Comparative Study)
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The research problem boils question is there in Riyadh organizational climate that enables them to do their work properly and whether there are differences between the government and private Riyadh depending on the organizational climate has sought Find measure: 1 regulatory climate for kindergarten 2. The difference between government and private Riyadh depending on the organizational climate. Limited research on the (200) parameter of the Riyadh government and private parameters for the year (20,142,015) In order to achieve the research objectives the researchers built a regulatory climate in accordance with the scientific steps to build a psychological scales measure After the formulation of climate regulation paragraphs of the (30) p

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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
A New Regimen in the Treatment of Psoriasis Using Oral Methotrexate
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Publication Date
Wed Mar 29 2023
Journal Name
Journal Of The College Of Education For Women
A Cognitive Linguistic Study of the Present Simple: An Experimental Study in the University of Baghdad
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Some research reports that cognitive grammar (CG) theory has good contributions to teaching English as a foreign language. In this research, the researchers seek to apply this theory and its principles when teaching the simple present tense to Iraqi students who face difficulties in differentiating between the multiple usages of this tense. To achieve this objective, the researchers have conducted an experimental study on a group of 60 Iraqi students in the University of Baghdad, College of Education for Women. Langacker’s (2003) theory has been adopted in the analysis of the cognitive relations to understand the common and different connections of these usages of the simple present. The study has concluded that the cognitive grammar t

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Publication Date
Sat Apr 13 2019
Journal Name
Journal Of The College Of Languages (jcl)
A Study of Collocation in English
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We used to think of grammar as the bones of the language and vocabulary as the flesh to be added given that language consisted largely of life generated chunks of lexis. This “skeleton image” has been proverbially used to refer to that central feature of lexis named collocation- an idea that for the first 15 years of language study and analysis gave a moment‟s thought to English classroom material and methodology.
The work of John Sinclair, Dave Willis, Ron Carter, Michael McCarthy, Michael Lewis, and many others have all contributed to the way teachers today approach the area of lexis and what it means in the teaching/learning process of the language. This also seems to have incorporated lexical ideas into the teaching mechanis

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