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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 May 10 2015
Journal Name
Al-academy
Performing processors of view between impressionism & superrealism (A comparative analysis): فريد خالد علوان
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Addressed the problem of the research is marked: (Performing processors for the time between Impressionism and superrealism) the concept of time and how to submit artwork. The search came in four sections: general framework for research and identified the research problem and the need for him. With an indication of the importance of his presence. Then determine the research objectives of (detection processors performing to the concept of time in works of art in each of Impressionism and superrealism. And a comparison between them to reveal similarities and differences), followed by the establishment of boundaries Find three (objectivity, the temporal and spatial) were then determine the terms related to the title. Then provide the theore

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Publication Date
Mon Dec 01 2014
Journal Name
2014 Ieee Symposium On Differential Evolution (sde)
Comparative analysis of a modified differential evolution algorithm based on bacterial mutation scheme
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A new modified differential evolution algorithm DE-BEA, is proposed to improve the reliability of the standard DE/current-to-rand/1/bin by implementing a new mutation scheme inspired by the bacterial evolutionary algorithm (BEA). The crossover and the selection schemes of the DE method are also modified to fit the new DE-BEA mechanism. The new scheme diversifies the population by applying to all the individuals a segment based scheme that generates multiple copies (clones) from each individual one-by-one and applies the BEA segment-wise mechanism. These new steps are embedded in the DE/current-to-rand/bin scheme. The performance of the new algorithm has been compared with several DE variants over eighteen benchmark functions including sever

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Publication Date
Fri Nov 01 2019
Journal Name
Journal Of Engineering
A Comparison Study of Brine Desalination using Direct Contact and Air Gap Membrane Distillation
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Membrane distillation (MD) is a hopeful desalination technique for brine (salty) water. In this research, Direct Contact Membrane Distillation (DCMD) and  Air Gap Membrane Distillation (AGMD) will be used. The sample used is from Shat Al –Arab water (TDS=2430 mg/l). A polyvinylidene fluoride (PVDF) flat sheet membrane was used as a flat sheet form with a plate and frame cell. Several parameters were studied, such as; operation time, feed temperature, permeate temperature, feed flow rate. The results showed that with time, the flux decreases because of the accumulated fouling and scaling on the membrane surface. Feed temperature and feed flow rate had a positive effect on the permeate flux, while permeate temperatu

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Publication Date
Mon Dec 30 2013
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Study of Water Flux through Forward Osmosis Membrane Using Brine\Fresh Water System
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The present work aims to improve the flux of forward osmosis with the use of Thin Film Composite membrane by reducing the effect of polarization on draw solution (brine solution) side.This study was conducted in two parts. The first is under the effect of polarization in which the flux and the water permeability coefficient (A) were calculated. In the second part of the study the experiments were repeated using a circulating pump at various speeds to make turbulence and reduce the effect of polarization on the brine solution side.
A model capable of predicting water permeability coefficient has been derived, and this is given by the following equations:
Z=Z+C.R.T/9.8(d2/D2+1) [Exp. [-9.8(d

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Publication Date
Tue Dec 01 2020
Journal Name
Baghdad Science Journal
A Competitive Study Using UV and Ozone with H2O2 in Treatment of Oily Wastewater
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          In this study, ultraviolet (UV), ozone techniques with hydrogen peroxide oxidant were used to treat the wastewater which is produced from South Baghdad Power Station using lab-scale system. From UV-H2O2 experiments, it was shown that the optimum exposure time was 80 min. At this time, the highest removal percentages of oil, COD, and TOC were 84.69 %, 56.33 % and 50 % respectively. Effect of pH on the contaminants removing was studied in the range of (2-12). The best oil, COD, and TOC removal percentages (69.38 %, 70 % and 52 %) using H2O2/UV were at pH=12. H2O2/ozone experiments exhibited better performance compared to

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Publication Date
Mon Jan 01 2024
Journal Name
Medical Research Archives
Genetic Polymorphism for the Gene Encoding Endoplasmic Reticulum Aminopeptidase-1 (ERAP-1) in Iraqi Patients with Ankylosing Spondylitis
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Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis affecting primarily the spine and pelvis. This study was aimed to investigate the relationship between the rs27044 polymorphism in Endoplasmic reticulum aminopeptidase-1 (ERAP-1) with the susceptibility and severity of AS correlated with some biochemical markers such as hematological parameter (Erythrocytes sedimentation rate (ESR)) and immunological parameters (C-reactive protein (CRP), Human leukocyte antigen-B27 (HLA-B27), Interlukin-6 (IL-6) and Interlukin-23 (IL-23)), and oxidative stress parameters (Glutathione (GSH) and Malondialdehyde (MDA)) in a sample of Iraqi population. A total of 60 blood samples were collected from AS patients requited Rhe

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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Suggestive Framework for Applying Performance and Programs Budget in Iraqi Government Units Environment
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Abstract

This research  aims to reform the Iraqi public budget through going into the challenges the budget faces in applying item-line budget in its preparation, implementation and control; which encourage extravagance and waste instead of rationalizing expenditures. This  is shown in the data analysis of Federal public budget laws in Iraq for the years from 2005 till 2013; there was a continuous increase in the aggregate public expenditures in the public budget for the years previously mentioned, as the public expenditures growth has reached into the percent 284.71% in 2013. In addition the public budget for these years (2005-2013) is being prepared with planned deficit without confirming that

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Publication Date
Mon Apr 04 2022
Journal Name
International Journal Of Early Childhood Special Educationpublishes
The impact of visual Management on the Strategic Acceleration; embedding knowledge as a Moderating Variable
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The research stems from its goal of identifying the impact of visual management on the strategic acceleration of business organizations and the state of this effect through the knowledge embedding in the Iraqi oil companies. The oil sector was tested, represented by (3) oil companies, and a sample of (151) individuals who participated in activating the visual management, distributed in higher management levels. The research relied on the descriptiveanalytical approach and the questionnaire was a main tool for collecting data and information. The results showed that visual management positively affects strategic acceleration. Moreover, This effect is amplified by the mediating role played by Embedding Knowledge.

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Publication Date
Sun Jun 11 2017
Journal Name
Al-academy
The approach of deliberation in the ontemporary Iraqi theater text - theatricality Afwah-as a odel
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The deliberative system of communicative studies is exposed to cultural openness, according to modern cultural studies, to establish a verbal language system that achieves reciprocal and cross-cultural relations. This research has examined the concept of deliberative approach in the contemporary Iraqi theater text by studying the deliberative system of text and its interrelationship with The stage of the verbal embodiment of the dramatic event, because the dramatic text achieves in its construction of racism, a deliberative approach between the verbal event and the language, and what later leads to the completion of the dramatic action. The research included four chapters. The first chapter was the systematic framework of the research, T

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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of College Of Education For Women
The Decisive Answers: A Pragmatic Linguistic Study
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يهتم هذا البحث بدراسة الأجوبة المسكتة,وهي أجوبة سريعة وحاسمة تقطع حجة الخصم وتفحمه وتغلقالحوار.وقد أرتكز البحث على منهجية تداولية تنظرإلى فاعلية الجواب المسكت في المحاورة وإنهائها من زواياإنجازية و حجاجية.وقد تكون البحث من ديباجة ممهدةوثلاثة مباحث.وسلطتالديباجةالممهدةالضوء علىمفهومالجواب المسكتوشيوعهفي كتب الأدبوالأخبارونوادر الكلاموكيف يمكن النظر لهبوصفه وحدة حوارية تنبنيمنها المحادثة؟أما المبحث ا

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