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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 Oct 01 2022
Journal Name
Journal Of Engineering
Parameters Affecting the Strength and Behavior of RC Dapped-End Beams: A Numerical Study
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The finite element method has been used in this paper to investigate the behavior of precast reinforced concrete dapped-ends beams (DEBs) numerically. A parametric investigation was performed on an experimental specimen tested by a previous researcher to show the effect of numerous parameters on the strength and behavior of RC dapped-end beams. Reinforcement details and steel arrangement, the influence of concrete compressive strength, the effect of inclined load, and the effect of support settlement on the strength of dapped-ends beams are examples of such parameters. The results revealed that the dapped-end reinforcement arrangement greatly affects the behavior of dapped end beam. The failure load decreases by 25% when

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Publication Date
Sun Mar 01 2020
Journal Name
Al-ustath Journal For Human And Social Sciences
HE SIGNIFICANCE OF FREUD’S THEORY THE UNCANNY IN NELLA LARSON’S PASSING: A PSYCHOANALYTIC STUDY
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ABSTRACT This study closely investigates the elements of Sigmund Freud’s theory “The Uncanny” in one of Larson’s most famous novels. Although the novel touches upon racial issues, the study explores the mysterious relationship between Irene and Clare based on the main features of Freud’s “The Uncanny,” which are represented by hidden sexual desire, envy, supernatural power, and double characters. The aspect of the sexual desire is indicated in the novel by sexual undertones expressed by Irene towards Clare’s physical features. Envy in the novel is expressed by Irene who shows resentful longing aroused by Clare’s possessions and qualities due to her passing to the white community. The aspect of omnipotence of thoughts is in

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Publication Date
Thu Jun 01 2023
Journal Name
مجلة اداب المستنصرية
The Concept of dialogue, it's importance, it's goals and it's character A descriptive Study
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Dialogue is one of the most important means of calling to the Creator, as it is one of the scientific and verbal activities carried out by a group of interlocutors to present ideas they believe in, and evidence and proofs that express their views and demonstrate the reason for their belief in them, In order to arrive at the truth or a radical solution to a specific problem, so the interlocutor should pay attention to this science, study it and its etiquette, because the purposeful dialogue requires that the funniest of them be the most knowledgeable and knowledgeable about the axis of the hadith, and the funniest must also be able to be convinced of the rule of difference of opinion that does not spoil the issue of friendly They must also c

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Publication Date
Sat Aug 16 2025
Journal Name
Al-adab Journal
Western Hermeneutics and Heritage: A Contemporary Study in the Debate of Understanding and Horizon.
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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
The Soil Effect on Subsidence in Area of Al- Karkh District A Geomorphologic Study
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Soil is considered one of the main factors of subsidence phenomena which
became continually happen in Baghdad (Ghazalia, Ameria, and Hay al-Amyl)
causing bad effects as shortage of drinking water, traffic jam and formation
swamps.
This thesis depends on soil study to a depth 15 meters, due to its
importance in subsidence. This done through specifying its chemical physical
properties.
Soil within Iraq climate, in case of water stopping for any reason it contract
and shrink away especially when it exposed to high pressure these factors
finally caused subsidence. In case of leakage underground water or that of
damaged water pipes this will contribute to chemical reactions which damage soil
structure and incr

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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of Engineering
Evaluating the Moisture Content Variation on Critical Strain of Geo-materials: A Case Study
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The tunnel’s stability during construction is a very important matter. Some methods have been proposed for stability evaluation, but the hazard warning levels (HWLs) are more applicable among these methods. Despite monitoring and applying HWLs, several collapses in Shibli twin tunnels in Iran have cast doubts on the accuracy of this criterion in the presence of water. In this study, the critical strains under different water contents were measured through uniaxial compressive strength tests on 11 different shale and marl samples. A comparison of laboratory tests and numerical results shows that the influence of the moisture content on the critical strain is negligible. In addition, the results show that there is no dir

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Study a bout the Epidemiology of Vulvo Vaginal Candidiasis (Candida spp.) in Baghdad City
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This Study was conducted to investigate vaginitis in women who live in Baghdad City. Results Revealed that Candida spp. were the causal agent of 38.5% of symptomatic cases the yeasts Candidaalbicans, C.glabrata, C.tropicalis, C.parapsilosis and C.krusei were isolated with the percentage of 38.1, 9.1, 3.9, 2.6, 1.3 respectively also there were 18% of women in control group carrying Candida spp. The direct smear method were not efficient because the percentage of infection was 17.5% comparing with the culture method the sensitivity of direct smear method was 45.5% The percentage of WBC to Epithelial cells was less than one in 76.6% of women.

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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of Clinical And Experimental Dentistry
The effect of osseodensification on implant stability and bone density: A prospective observational study
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Background: The aims of this study were to evaluate the effect of implant site preparation in low-density bone using osseodensification method in terms of implant stability changes during the osseous healing period and peri-implant bone density using CBCT. Material and methods: This prospective observational clinical study included 24 patients who received 46 dental implants that were installed in low-density bone using the osseodensification method. CBCT was used to measure the bone density pre- and postoperatively and implant stability was measured using Periotest® immediately after implant insertion and then after 6 weeks and 12 weeks postoperatively. The data were analyzed using paired t-test and the probability value <0.05 was conside

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Publication Date
Tue Apr 14 2020
Journal Name
Modern Sport
The Effect of Using the Bybee Strategy(5ES) according to Brain Control Patterns in Learning a Kinetic Series on Floor exercises in Artistic Gymnastics for men
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The aim of this study to identify patterns of cerebral control (right and left) for second grade students in the collage of physical education and sports science of the University of Baghdad, as well as identify the definition of theThe Effect of Using the Bybee Strategy(5ES) according to Brain Control Patterns in Learning a Kinetic Series on Floor exercises in Artistic Gymnastics for menمجلة الرياضة المعاصرةالمجلد 19 العدد 1 عام 2020effect using the (Bybee) strategy (5ES) according to brain control patterns inlearning a Kinetic series on floor exercises In artistic gymnastics for men, andidentify the best combination between the four research groups learn, use Finderexperimental method research sample consi

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Publication Date
Sun Oct 31 2021
Journal Name
Iraqi Geological Journal
Optimizing Water Injection Performance by Using Sector Modeling of the Mishrif Formation in West Qurna-1 Oil Field, Southern Iraq
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The regular job of a reservoir engineer is to put a development plan to increase hydrocarbon production as possible and within economic and technical considerations. The development strategy for the giant reservoir is a complex and challenging task through the decision-making analysis process. Due to the limited surface water treatment facility, the reservoir management team focuses on minimizing water cut as low as possible by check the flow of formation and injected water movement through the Mishrif reservoir. In this research, a representative sector was used to make the review of water injection configuration, which is considered an efficient tool to make study in a particular area of the entire field when compared with the ful

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