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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 Nov 30 2018
Journal Name
Iop Conference Series: Materials Science And Engineering
Estimating the PVT Properties for Crude Oil from a Southern Iraqi Oil Field
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Publication Date
Sun Apr 01 2012
Journal Name
American Journal Of Applied Sciences
A New Strategy for Signaling Overhead Reduction in the Proxy Mobile IPv6 Protocol
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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of Planner And Development
Urban sustainability assessment for the urban renewal project in Al Shawaka a rea
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Sustainability is a major demand and need pursued by cities in all areas of life due to the environmental, social and economic gains they provide, especially in the field of city planning and urban renewal projects that aim to integrate the past, present and future.

 

The research aims to evaluate the Haifa Street renewal project, and Al-Shawaka district, one of the Baghdad districts located next to Al-Karkh, was elected by comparing the sustainability indicators of urban renewal with the reality of the situation through a field survey and questionnaire form and focusing on the social and economic impacts and environmental for the project on the study area. To reach the most important conclusions and recommendations

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Publication Date
Wed Mar 01 2023
Journal Name
Journal Of Engineering
Recycled Concrete Aggregated for the use in Roller Compacted Concrete: A Literature Review
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The using of recycled aggregates from construction and demolition waste (CDW) can preserve natural aggregate resources, reduce the demand for landfill, and contribute to a sustainable built environment. Concrete demolition waste has been proven to be an excellent source of aggregates for new concrete production. At a technical, economic, and environmental level, roller compacted concrete (RCC) applications benefit various civil construction projects. Roller Compacted Concrete (RCC) is a homogenous mixture that is best described as a zero-slump concrete placed with compacting equipment, uses in storage areas, dams, and most often as a basis for rigid pavements. The mix must be sufficiently dry to support

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Publication Date
Mon Jun 01 2020
Journal Name
مجلة العلوم و التكنولوجية للنشاطات البدنية و الرياضية/ الجزائر
The effect of using the five-finger strategy on learning movement chain on a balance beam in the artistic gymnastics of women
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Abstract: The aim of the research identify the effect of using the five-finger strategy in learning a movement chain on the balance beam apparatus for students in the third stage in the College of Physical Education and Sports Science, as well as to identify which groups (experimental and controlling) are better in learning the kinematic chain on the balance beam device, has been used The experimental approach is to design the experimental and control groups with pre-and post-test. The research sample was represented by third-graders, as the third division (j) was chosen by lot to represent the experimental group, and a division Third (i) to represent the control group, after which (10) students from each division were tested by lot to repr

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Strategic Risk's Variation as a function of Competitive Intelligence Investment - An applied research on some Iraqi's manufacturing Companies –
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ABSTRUCT

          The main aim of this research has been associated with the study of relationship between competitive intelligence and strategic risk, and to deduct their specific trends, which are interpreted as predicted by research hypotheses according to a review of literature including prior studies. The basic theme  of these hypotheses is related to the probability that declining levels of strategic risk and competitive positions of industrial companies is dependent upon the growing capacity to stay ahead of competitors in the market.

    A purposive non-random

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Publication Date
Wed Sep 15 2021
Journal Name
Journal Of Baghdad College Of Dentistry
Salivary Cortisol as a Stress Biomarker and Total Viable Count of Salivary Bacterial Microbiome among COVID-19 Patients
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Background: The COVID-19 virus outbreak had a massive effect on many parts of people's lives, as they were advised to quarantine and lockdown to prevent the virus from spreading, which had a big impact on people's mental health, anxiety, and stress. Many internal and external factors lead to stress. This negatively influences the body's homeostasis. As a result, stress may affect the body's capacity to use energy to defend against pathogens. Many recent investigations have found substantial links between human mental stress and the production of hormones, prohormones, and/or immunological chemicals. some of these researches have verified the link between stress and salivary cortisol levels. The aim of this study is to measure salivary corti

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Engineering
Prediction of the Effect of Using Stone Column in Clayey Soil on the Behavior of Circular Footing by ANN Model
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Shallow foundations are usually used for structures with light to moderate loads where the soil underneath can carry them. In some cases, soil strength and/or other properties are not adequate and require improvement using one of the ground improvement techniques. Stone column is one of the common improvement techniques in which a column of stone is installed vertically in clayey soils. Stone columns are usually used to increase soil strength and to accelerate soil consolidation by acting as vertical drains. Many researches have been done to estimate the behavior of the improved soil. However, none of them considered the effect of stone column geometry on the behavior of the circular footing. In this research, finite ele

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Publication Date
Sun Oct 01 2017
Journal Name
Journal Of Educational And Psychological Researches
Factors associated with the phenomenon of marriage outside the court And the consequences of it A field study in Sadr City
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Marriage outside the court is a manifestation of the oppression that women are subjected to in Iraq its seriousness comes out of the consequences that it leads to The. It overlooks the age of the girl and her marriage in younger age or coerced to marry as it leads to neglecting the affordability of marital relationship as long as the marriage does not have any legal or material consequences. The present study aims to detect Characteristics of both wives, husbands and families Who agree to marry her daughters outside the court. And the reasons that lead them to marry outside the courts. It also aims to provide information on the circumstances of marriage and reasons for refusing to ratify it in court. The study was based on the sample soc

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Publication Date
Thu Dec 24 2020
Journal Name
Psychology And Education
The Use of Ergative Verbs to Background the Role of the Agent in two Selected Short Stories: A Syntactico-Semantic Study
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The study explores the use of ergative verbs in constructing clauses and their impact on the backgrounding of the agent's role in two selected short stories. Contrary to hypothesis No. 1, the research indicates that changes in sentence patterns don't affect the meaning of the process. Additionally, hypothesis No. 2 is refuted as the middle structure is found to highlight the agent's role in the science fiction short story, Terra Infirmum, rather than concealing it as hypothesized for "The Invisible Man." The analysis uncovers that writers utilize ergative processes to narrate stories in various ways, including transitive/active voice, intransitive/active voice, and transitive/passive voice. Furthermore, the findings suggest that writers emp

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