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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 Dec 17 2022
Journal Name
Journal Of The College Of Languages (jcl)
The Use of the Definite article in the Ottoman Turkish Language in the Fourteenth and Seventeenth Centuries: Qaboos Namah and Mazaki Collection as a Model: '' Kabusnâme ve Mezâkî Divanı Örneğinde ''14. ve 17. Yüzyılarda Osmanlı Türkçesinde Harf-i Ta'rifin Kullanması Üzerine Bir İnceleme
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The Turks used the Ottoman Turkish language from the thirteenth century to the twentieth century.  During this period and under the influence of Islamic civilization, a large number of words and structures were used from the Arabic and Persian languages, Therefore, many Arabic grammatical structures were used in the Ottoman Turkish language, such as the definite article simply because it was widely used.

The paper is concerned with the use of the Arabic definite article in the Ottoman Turkish language, and the aim of this contrastive study is to find out the similarities and differences between the two languages ​​in terms of meaning and structure. Since linguistic studies depend on the practical side or applied approach, two

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Publication Date
Thu Sep 08 2022
Journal Name
Al-khwarizmi Engineering Journal
Assessment of Ornamental Plants Tolerance for Acute Exposure of Acetaminophen and Methylparaben in Constructed Wetlands- a Preliminary Study
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The study aims to select suitable ornamental plant species that can survive relatively with high concentrations of acetaminophen and methylparaben in constructed wetlands. Alternanthera spp, Asparagus aethiopicus and Chlorophytum comosum are examined to withstand three initial concentrations, 20, 100 and 200 mg/L of acetaminophen and methylparaben. A total of 21 plastic pails with each 3 L capacity consisting of nine pails are used for each pharmaceutical and personal care products (PPCPs) compounds (acetaminophen and methylparaben) for three ornamental plants (Alternanthera spp, Asparagus aethiopicus and Chlorophytum comosum), with three pails as plant controls. The results reveales

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Publication Date
Sun Jun 16 2019
Journal Name
Al–bahith Al–a'alami
News frames for the phenomenon of terrorism in international satellite channels directed in Arabic An analytical study of the main news bulletins in the Russian channel today 1/2/31/5/2018
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International satellite channels in Arabic are targeted to the region with their news bulletins and their innovative programs, attracting the interest of the Arab viewers in their news articles and programs with new ideas and methods as well as high technology in the production and synthesis of videos. Therefore, they work on framing the above, And the media policy that governs, so focused the problem of the study to try to answer the question of the President is how to frame the international satellite channels in Arabic to the phenomenon of terrorism? What are the aspects that are working to highlight and aspects that try to hide? The study adopted the survey methodology for the main news bulletins in the Russian channel today for the

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Publication Date
Sat Jan 01 2022
Journal Name
3rd International Scientific Conference Of Alkafeel University (iscku 2021)
Investigations for the critical vehicle velocities on a curved path
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􀀨􀀅􀀆􀀔􀀜􀀄􀀂􀀆􀀈􀀓􀀌􀀩􀀏􀀆􀀉􀀅􀀆􀀉􀀅􀀉􀀚􀀝􀀔􀀄􀀗􀀉􀀚􀀆􀀂􀀓􀀚􀀁􀀔􀀄􀀓􀀅􀀆􀀄􀀂􀀆􀀔􀀓􀀆􀀃􀀂􀀔􀀄􀀟􀀉􀀔􀀃􀀆􀀔􀀜􀀃􀀆􀀛􀀃􀀜􀀄􀀗􀀚􀀃􀀆􀀗􀀌􀀄􀀔􀀄􀀗􀀉􀀚􀀆􀀂􀀘􀀃􀀃􀀊􀀂􀀆􀀓􀀖􀀆􀀓􀀛􀀃􀀌􀀔􀀁􀀌􀀅􀀄􀀅􀀕􀀢􀀆􀀪􀀜􀀃􀀆􀀄􀀅􀀛􀀃􀀂􀀔􀀄􀀕􀀉􀀔􀀄􀀓􀀅􀀂􀀆 􀀉􀀌􀀃􀀆􀀙􀀉􀀂􀀃􀀊􀀆􀀓􀀅􀀆􀀉􀀁􀀔􀀓􀀟􀀓􀀙􀀄􀀚􀀃􀀆􀀚􀀉􀀔􀀃􀀌􀀉􀀚􀀆􀀂􀀘􀀉􀀗􀀃􀀆􀀟􀀄􀀊􀀂􀀔􀀆􀀔􀀜􀀃􀀆􀀗􀀃􀀅􀀔􀀃􀀌􀀚􀀄􀀅􀀃􀀂􀀆􀀓􀀖􀀆􀀔􀀜􀀃􀀆􀀙􀀉􀀂􀀃􀀆

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Publication Date
Mon Sep 03 2018
Journal Name
Al-academy
A new vision for the classic in contemporary fashion designResearch
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        fashion designers who have benefited greatly from the mobilization of ancient aesthetic ideas in the heritage of the people and guaranteed in their productions so that there is no change In the aesthetic value created by the designers of the research in the ancient heritage to find new signs that reflect the connection of man to the present as the aesthetic value of all the man created by the designs of fabrics and fashion through the ages      The problem of research was determined in the absence of a precise understanding of the nature of classical thought in fashion and the absence of a clear perception of the sustainability of this thought in contemporary fashion. He

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Publication Date
Fri Mar 01 2019
Journal Name
Al-khwarizmi Engineering Journal
A Finite Element Analysis for the Damaged Rotating Composite Blade
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In this paper, the finite element method is used to study the dynamic behavior of the damaged rotating composite blade. Three dimensional, finite element programs were developed using a nine node laminated shell as a discretization element for the blade structure (the same element type is used for damaged and non-damaged structure). In this analysis the initial stress effect (geometric stiffness) and other rotational effects except the carioles acceleration effect are included.  The investigation covers the effect speed of rotation, aspect ratio, skew angle, pre-twist angle, radius to length, layer lamination and fiber orientation of composite blade. After modeling a non-damaged rotating composite blade, the work procedure was to ap

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Publication Date
Wed Apr 01 2020
Journal Name
Civil Engineering Journal
Model Development for the Prediction of the Resilient Modulus of Warm Mix Asphalt
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Increasing material prices coupled with the emission of hazardous gases through the production and construction of Hot Mix Asphalt (HMA) has driven a strong movement toward the adoption of sustainable construction technology. Warm Mix Asphalt (WMA) is considered relatively a new technology, which enables the production and compaction of asphalt concrete mixtures at temperatures 15-40 °C lower than that of traditional hot mix asphalt. The Resilient modulus (Mr) which can be defined as the ratio of axial pulsating stress to the corresponding recoverable strain, is used to evaluate the relative quality of materials as well as to generate input for pavement design or pavement evaluation and analysis. Based on the aforementioned preface, it is

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Publication Date
Tue Nov 19 2019
Journal Name
Iranian Journal Of Science And Technology, Transactions A: Science
Systematic Study of the Nuclear Structure for Some Exotic Nuclei Using Skyrme–Hartree–Fock Method
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The ground state charge, neutron, proton and matter densities, the associated nuclear radii and the binding energy per nucleon of 8B, 17Ne, 23Al and 27P halo nuclei have been investigated using the Skyrme–Hartree–Fock (SHF) model with the new SKxs25 parameters. According to the calculated results, it is found that the SHF model with these Skyrme parameters provides a good description on the nuclear structure of above proton-rich halo nuclei. The elastic charge form factors of 8B and 17Ne halo nuclei and those of their stable isotopes 10B and 20Ne are calculated using plane-wave Born approximation with the charge density distributions obtained by SHF model to investigate the effect of the extended charge distributions of proton-rich nucl

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Publication Date
Wed Sep 01 2021
Journal Name
Baghdad Science Journal
Fuzzy-assignment Model by Using Linguistic Variables
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      This work addressed the assignment problem (AP) based on fuzzy costs, where the objective, in this study, is to minimize the cost. A triangular, or trapezoidal, fuzzy numbers were assigned for each fuzzy cost. In addition, the assignment models were applied on linguistic variables which were initially converted to quantitative fuzzy data by using the Yager’sorankingi method. The paper results have showed that the quantitative date have a considerable effect when considered in fuzzy-mathematic models.

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Publication Date
Sun Sep 01 2013
Journal Name
Baghdad Science Journal
Comparison study of Interleukin-1 alpha between Unstable Angina and Acute Myocardial Infarction patients
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Multiple studies support a role for inflammation in the pathogenesis of coronary atherosclerosis and unstable cardiac syndromes. However, of the known pro-inflammatory cytokines, only elevated plasma levels of interleukin-6(IL-6) have been linked to Unstable Angina. We sought to examine the plasma levels of other major proinflammatory cytokines in similar clinical settings patients with unstable angina and acute myocardial infarction and the relationship extent between them. This study aimed to investigate and compare the level of IL-1 in Unstable Angina and Acute Myocardial Infarction patients. Thirty patients with unstable angina and thirty patients with Acute Myocardial Infarction, also thirty healthy individual as control were included

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