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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
Wed May 02 2012
Journal Name
Journal Of Planner And Development
The Effect of Time and Place Dimensions on Changing the Quality Dimensions of Sizes of Cities: A Case Study (Baghdad city)
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The city has normal natural state, and the man has a usual movement, change and search for the new .Also, the city has a usual change and transform in its time, place and quality (sizes)structures. The city has a solid memory diving into the past and the future and reflects The real present, and this memory has a timing layers change into real materialistic place making the city has accumulated overlapping circles which is hard to break u , and it broadcasts the lockup timing density ,in which there is no visual record precisely, it is just like((the social record)) that evaluates the un visual relationships between the components and parts of the city (community and form) in a visual quiet exhibition and transform change inside.

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Publication Date
Thu Feb 06 2020
Journal Name
Political Sciences Journal
Self-immuniztion: integration of Russian strategic performance a study in the geopolitical orientation circles "of the stage of president putin"n
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In the period after the collapse of the Soviet Union in 1991, the Federal Republic of Russia witnessed a setback in the overall strategic performance of the country, as it went through a stage of performance flop between the orientation towards Europe in the era of President Boris Yelsen (1991-1999), or the change of direction towards Eurasia, as the Russian Federation managed After President Vladimir Putin assumed power in 2000, from rebuilding the same state and preserving national unity and social cohesion, as well as building a phased military doctrine that made clear moves in Russian strategic thought and future directions towards regions of eternal importance in Russian strategic perception Lack of a set of motivations based on it:

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Publication Date
Sun Feb 05 2023
Journal Name
مجلة تكريت للعلوم الادارية والاقتصادية
The role of strategic auditing of human resources management in crystallizing organizational capabilities: A prospective study at the University of Baghdad
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دور التدقيق الاستراتيجي لإدارة الموارد البشرية في بلورة القدرات التنظيمية دراسة استطلاعية في رئاسة جامعة بغداد

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Publication Date
Sat Dec 31 2022
Journal Name
Al-kindy College Medical Journal
Assessment of Serum Level of Protein Carbonyl as a Marker of Protein Oxidation in Patients with Type 2 Diabetes Mellitus
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Background: Diabetes mellitus is a chronic disease with an increasing prevalence worldwide and characterized by an increase in oxidative stress and inflammation. The most important factor that is responsible for oxidative stress and production of reactive oxygen species (ROS) is hyperglycemia. The major targets of ROS are proteins. The most common and widely used biomarker of severe oxidative protein damage is protein carbonyl content.

The study was designed to assess the serum level of protein carbonyl as a marker of protein oxidation in patients with type 2 diabetes mellitus and to evaluate the effect of age, body weight, waist circumference, diabetic control and disease duration on the level

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Publication Date
Tue Nov 09 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Strategic leadership and its role in achieving competitiveness in industrial establishments": "A field study in Bashir Al-Siksik & Co. for the manufacture of sanitary and plastic tools
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This study aims to know the role of strategic leadership to achieving competitiveness in industrial establishments by identifying the respondents’ perceptions about the level of availability of dimensions of leadership strategies (creativity and innovation, risk tolerance, available opportunities) in Bashir Al-Siksek & Partners Company for the manufacture of sanitary and plastic ware in Gaza strip

To achieve this, a questionnaire was developed and distributed to a sample of managers, auditors, accountants, and administrative employees in the study sample company. The questionnaire tool was distributed to 60 employees and employees, of which (52) were retrieved, or 86.6%, and (8) were excluded for la

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of The College Of Education For Women
Forced Displacement during the Syrian Forced Displacement during the Syrian Crisis, and its Impact on Jaramana’s Children's Education: A Field Study , and its Impact on Jaramana’s Children's Education: A Field Study: نهال ريحاوي جلب , قاسم الربداوي
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The study aims to examine the problem of forced displacement and its social and economic problems in light of the Syrian crisis. Such an aim helps to know the difficulties and challenges facing the children of displaced families in learning, and the reasons for their lack of enrolment. It also clarifies whether there are significant statistical differences at  among the attitudes of the children of the displaced families towards education regarding the following variables: (the work of the head of the family, the economic level of the family, and the work of the children). The study has adopted the descriptive-analytical approach;  a questionnaire was adopted as a tool to collect information. The study was applied to a sample o

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Publication Date
Tue Feb 24 2026
Journal Name
Journal Of Administration And Economics
Using the Maximum Likelihood Method with a Suggested Weight to Estimate the Effect of Some Pollutants on the Tigris River- City of Kut
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The aim of this research is to use robust technique by trimming, as the analysis of maximum likelihood (ML) often fails in the case of outliers in the studied phenomenon. Where the (MLE) will lose its advantages because of the bad influence caused by the Outliers. In order to address this problem, new statistical methods have been developed so as not to be affected by the outliers. These methods have robustness or resistance. Therefore, maximum trimmed likelihood: (MTL) is a good alternative to achieve more results. Acceptability and analogies, but weights can be used to increase the efficiency of the resulting capacities and to increase the strength of the estimate using the maximum weighted trimmed likelihood (MWTL). In order to perform t

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Publication Date
Fri Dec 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
Effect of Addition Different Levels of Kojic Acid and Sodium Alginate as a substitutes of conventional Antibiotic on the Characteristics of Cryopreserved Semen of Buffalo Bulls
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Abstract<p>This experiment examined the effects of adding sodium alginate and KOJIC acid as substitutes of Conventional antibiotics to soybean lecithin extender on the characteristics of cryopreserved and frozen buffalo bull semen, as well as evaluation of their additions as antibiotics that to help lowering the microbial load. Following the collection and dilution of in the soybean lecithin extender, the experimental treatments were separated into five groups, as follows: T1: (control-) without adding any antibiotics; T2: (control+) adding the conventional antibiotics Gentamicin 0.4 IU and Tylosin 0.08 IU per 100 ml; T3: adding Kojic acid at (0.06 g/L) T4: adding sodium alginate at (0.6 mg/mL)T</p> ... Show More
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Publication Date
Sat Nov 12 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The relationship of salary localization and the growth of bank deposits: (applied research for a sample of private banks)
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The research problem consisted in answering the question that revolves around whether there is a relationship to the settlement of salaries with the growth of bank deposits? The research also aimed to provide some initial solutions to improve the role of salary localization, in terms of reviewing the concept of electronic payment systems, its tools and channels, and then identifying the concept of salary localization, its importance, objectives and obstacles to its application, and then analyzing the reality of the state of the settlement of salaries and bank deposits for the research sample banks, which are each of the bank (Ashur International, Business Bay, the Iraqi Middle East for Investment, the Iraqi National, Development and the

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Publication Date
Thu Nov 12 2020
Journal Name
Journal Of Petroleum Research And Studies
Production Optimization for Natural Flow and ESP Well A Case Study on Well NS-5 Mishrif Formation-Nasriya Oil Field
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As the reservoir conditions are in continuous changing during its life, well production rateand its performance will change and it needs to re-model according to the current situationsand to keep the production rate as high as possible.Well productivity is affected by changing in reservoir pressure, water cut, tubing size andwellhead pressure. For electrical submersible pump (ESP), it will also affected by numberof stages and operating frequency.In general, the production rate increases when reservoir pressure increases and/or water cutdecreases. Also the flow rate increase when tubing size increases and/or wellhead pressuredecreases. For ESP well, production rate increases when number of stages is increasedand/or pump frequency is

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