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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
Fri Feb 28 2025
Journal Name
Bmc Psychology
Delving into the Elements Impacting Treatment Acceptance among patients with Substance Use Disorder using Health Belief Model: a qualitative study
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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of Central European Agriculture
Biofertilizer (EM-1) effect on growth and yield of three bread wheat cultivars
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Farmers keep trying to avoid using chemical fertilizer without losing high yield. A field experiment was conducted in the fields of Agriculture College, University of Baghdad during winter seasons of 2015 and 2016 to investigate the response of three bread wheat (Triticum aestivum L.) cultivars (Ibaa99, Abu-Ghraib3 and Buhooth22) to the frequency of spraying with biofertilizer (EM-1) (one time at tillering stage, twice at tillering and stem elongation stages and three times at tillering, stem elongation and booting stages) in addition to the control (without spraying), to the increase of grain yield. Randomized complete block design (RCBD), in split plots arrangement and four replications, was used. Spraying treatments were placed as main p

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Publication Date
Fri Jan 01 2021
Journal Name
Materials Today: Proceedings
Study the electronic and spectroscopic properties of ALxB7-XN7 Wurtzoids as a function of size and concentration using density functional theory
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Publication Date
Fri Jan 01 2021
Journal Name
Materials Today: Proceedings
Study the electronic and spectroscopic properties of ALxB7-XN7 Wurtzoids as a function of size and concentration using density functional theory
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Electronic properties including (bond length, energy gap, HOMO, LUMO and density of state) as well as spectroscopic properties such like infrared, Raman scattering, force constant, reduced mass and longitu- dinal optical mode as a function of frequency are based on size and concentration of the molecular and nanostructures of aluminum nitride ALN, boron nitride BN and AlxB7-XN7 as nanotubes has calculated using Ab –initio approximation method dependent on density functional theory and generalized gradient approximation. The geometrical structure are calculated by using Gauss view 05 as a complementary program. Shows the energy gap of ALN, BN and AlxB7-XN7 as a function of the total number of atoms , start from smallest molecule to reached

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Publication Date
Fri Jul 01 2016
Journal Name
Al–bahith Al–a'alami
Semiotics of Sufi Texts- Poets of Al Qasr and Al-Asr journals as a Model
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In a common language based on interpretation and diagnosis in the symbols and signs, the subject of Sufism and artistic semiotics is manifested in the construction and intensity of the reading of the text and the dismantling of its intellectual systems.
The emergence of Sufism in its religious features and the spiritual revelations related to the divine love of life in absolute reality, And images and language in a stream of intellectual and artistic unique and harmonious communicates with the subject of the themes of the Arab literature and its implications, but it is separated by a special entity signals and symbols related to the mysticism and worship.
    The unleashing of the imagination and the diagnosis,

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Publication Date
Mon Feb 16 2026
Journal Name
Al–bahith Al–a'alami
Foreign Propaganda in the Electronic Press about the Syrian Crisis A Comparative Study of the Sites of Russia Today and Alhurra - A research drawn from a Master Degree thesis
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The research problem lies in the ambiguity of the usage of propaganda contents by two main media outlets (the Russian RT and American Alhurra) in their news coverage of the Syrian crisis through their websites and the methods used by them to convince users taking into account the mutual propaganda conflict between the United States and Russia in the war against Syria. The objectives of the research can be represented by the following: investigating the contents of American and Russian electronic propaganda towards Syrian crisis.
• Identifying the contents that received most of the coverage in the Syrian crisis by the two news outlets.
• Identifying the terms and phrases that have been most used by the websites of RT and Alhurr

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Publication Date
Sun Feb 10 2019
Journal Name
Iraqi Journal Of Physics
A study of the effect of silica particles addition on some physical properties of PVC as a packaging material
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In this work, varying compositions of SiO2 micro filler were added
with the Polyvinyl Chloride (PVC) and samples have been prepared
using film casting technique. The results have been analyzed and
compared for PVC samples with (1 wt%, 3 wt%, 5 wt% and 10 wt%)
SiO2 micro filler. Mechanical characteristics such as tensile strength,
elongation at break and Young`s modulus were measured for all the
samples, where the tensile strength was increased from 8.39 Mpa for
purified PVC to 16 Mpa for 3% SiO2/PVC composite. Also, thermal
conductivity measurement values illustrated that composite materials
have a good thermal insulation at 10 wt. %, thermal conductivity was
decreased from 0.1684 W/m.

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Publication Date
Sat Jun 25 2022
Journal Name
Al-mağallaẗ Al-šāmilaẗ Li-l-ḥuqūq
The Intent to Harm Others as a Form of Abuse of Rights – A Study in Light of U.S. Law
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In a world of limited space, the owners are always surrounded by others next to them, and, consequently, there is hardly any activity which the owner may exercise on his land which would not affect the other owners. If he builds a building, that building may block the sun's rays or the air from the buildings next to it and owned by other people. And if he runs a business, the lands adjacent to that business may be overburdened with the accompanying noise or traffic. If oil is prospected in a land, the neighboring lands may be deprived of oil or their owners may be exposed to toxic fumes. Hence the importance of researching the intention of harming others, as it is one of the most important forms of abuse in the use of the right (especially

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Publication Date
Fri Dec 01 2017
Journal Name
British Journal Of Oral And Maxillofacial Surgery
A novel approach for the three-dimensional evaluation of facial asymmetry of unilateral cleft lip and palate patients (UCLP)
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Publication Date
Fri Jun 30 2023
Journal Name
Iraqi Journal Of Science
Assessing the Potentiality of Using CXCL9 as A Predictive Biomarker for Acute and Chronic Toxoplasmosis, and Study the Correlation Between CXCL9, Toxoplasmosis and Thyroid Disorder in These Cases
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     Background:  Chemokine (C-X-C motif) ligand (CXCL9) has an important role recruiting the T-lymphocytes and immune response after infection by inducing T-cells accumulation around the areas associated with infections. However, this role is poorly known in relation with Toxoplasma gondii infection and also in association with thyroid hormones, which the present study is focused on. Methods: Eighty-seven women were included in this study for the period between September 2021 and February 2022. Blood samples of uninfected healthy pregnant, in addition to aborted and pregnant women infected with toxoplasmosis, were collected. Sera were then obtained and stored at -10°C. Toxo-latex agglutination test was done, followed by detec

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