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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 Jun 30 2021
Journal Name
College Of Islamic Sciences
العربية Atheism A study in the most important foundations of atheism, and the most prominent suspicions of its advocates: دراسة في أهمّ مرتكزاته، وأبرز شبهات دُعاته
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Atheism is one of the most dangerous absurd doctrines that have swept the world in the modern era. Its strength lies in the bodies that stand behind it and adopt its ideologies which are accompanied by the tremendous media momentum of the theses of its supporters based on scientific and non-scientific levels. And since the denial of the existence of the Creator is the main focus and central point which the atheists based their view towards the universe, life and man, this humble research came to discuss the claim of the existence of the world by pure chance, and try to explain this scientifically through the theory of natural selection and survival of the fittest developed by the English biologist Charles Darwin. The resea

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Publication Date
Sun Feb 28 2021
Journal Name
Journal Of Economics And Administrative Sciences
Availability Assessment of theManaging the Audit Program. According to the Specification Standard (ISO 19011:2018): A case study in Ministry of Construction Housing and General Municipalities
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The research aims to study the reliability of government institutions, including the audit directors, which are one of the most important oversight formations in the Ministry of Construction, Housing and Public Municipalities, on which the responsibility for comprehensive auditing of all the Ministry's (municipalities) formations falls on the Managing the Audit Program according to the specification (ISO 19011: 2018) to improve the audit performance which requires compliance with the application of the audit management system in accordance with the standard Specification (ISO 19011: 2018), depending on the methodology of the case study, and using of checklists, which were chosen ac

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Publication Date
Wed Jan 01 2020
Journal Name
Proceedings Of The 2020 2nd International Conference On Sustainable Manufacturing, Materials And Technologies
The impact of toxicant on the food chain ecological model
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Publication Date
Fri Jan 13 2023
Journal Name
Atmosphere
Impact of North African Sand and Dust Storms on the Middle East Using Iraq as an Example: Causes, Sources, and Mitigation
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This study aims to determine the reasons for the increase in the frequency of sand and dust storms in the Middle East and to identify their sources and mitigate them. A set of climatic data from 60 years (1960–2022) was analyzed. Sand storms in Iraq are a silty sand mature arkose composed of 72.7% sand, 25.1% silt, and 2.19% clay; the clay fraction in dust storms constitutes 70%, with a small amount of silt (20.6%) and sand (9.4%). Dust and sand storms (%) are composed of quartz (49.2, 67.1), feldspar (4.9, 20.9), calcite (38, 5), gypsum (4.8, 0.4), dolomite (0.8, 1.0), and heavy minerals (3.2, 6.6). Increasing temperatures in Iraq, by an average of 2 °C for sixty years, have contributed to an increase in the number of dust storm

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Publication Date
Mon Dec 28 2020
Journal Name
Journal Of Physical Education
Time of Motor Response To Stimuli (Auditory and Visual) and Its relationship with Blocking Accuracy In Volleyball
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The research aim at identifying the time of motor response to auditory and visual stimuli as well as identifying the accuracy of blocking and finding the relationship between motor repose time and blocking accuracy. The community was (7) primer soccer league of 2019 – 2020 and the subjects were (24) volleyball players from Al Jaish and Al Shorta clubs ten players from Al Shorta club performed the pilot study. The researchers used the descriptive method and the data was collected and treated using SPSS. The results showed a significant relationship between response time and blocking accuracy. The researchers recommended concentrating on applying scientific principles for developing time of motor response in a manner suitable for bl

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Publication Date
Tue Aug 24 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A plan for transportation and distribution the products based on multi-objective travelling salesman problem in fuzzy environmental
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Transportation and distribution are the most important elements in the work system for any company, which are of great importance in the success of the chain work. Al-Rabee factory is one of the largest ice cream factories in Iraq and it is considered one of the most productive and diversified factories with products where its products cover most areas of the capital Baghdad, however, it lacks a distribution system based on scientific and mathematical methods to work in the transportation and distribution processes, moreover, these processes need a set of important data that cannot in any way be separated from the reality of fuzziness industrial environment in Iraq, which led to use the fuzzy sets theory to reduce the levels of uncertainty.

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Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
Studying the Changes in Solar Radiation and Their Influence on Temperature Trend in Iraq for a Whole Century
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Most studies indicated that the values ​​of atmospheric variables have changed from their general rates due to pollution or global warming etc. Hence, the research indicates the changes of direct solar radiation values ​​over a whole century i.e. from 1900 to 2000 depending on registered data for four cities, namely (Mosul - Baghdad - Rutba - Basra. Moreover, attemptsto correlate the direct solar radiation with the temperature values have been ​​recorded over that period. The results showed that there is a decreasing pattern of radiation quantities over time throughout the study period, where the value of direct radiation over the city of Baghdad 5550 w/m2 was recorded in the year 1900, but this ratio decreased cle

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Publication Date
Sun Feb 04 2018
Journal Name
Journal Of The College Of Education For Women
Phrenic nerve paralysis during cryoballoon ablation for atrial fibrillation: A comparison between the first- and second-generation balloon
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The present study deals with the effect of teaching speaking Strategies (SS) on EFL Iraqi College students. The use of speaking strategies not only solves learners’ communication problems, but also enhances the learner’s interaction in target language, and improves their oral proficiency .The aim of the study is to find out the effect of teaching SS used by EFL College students .The learner of the first stage is population of the study at the Department of English, College of Education /Ibn-Rushd .The sample consists of (60) students distributed on experimental group(A) as well as control group(B) each group contains (30) students . In order to achieve the aim of the study, questionnaire has been constructed to be taught on the experime

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Publication Date
Sat Jan 09 2016
Journal Name
مجلة العلوم التربوية والنفسية
Hill, the Employment of a Specimen in the Teaching of Arabic Grammar
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The construction process of reception containing rebuild educated new gloss within the context of real-time knowledge with previous experience and learning environment, accounting for all of the real experiences and information beside Education backbones structural climate (olive 0.2002: p. 212 .) Based on two basic principles - : I: - The natural science that we do know from our experiences, we can not say for sure Bhakaigah realism and clearly, but built by creative minds of certain interpretations be applicable in light of our expectations. Other: - The knowledge built effectively active learner who adapts new knowledge with the conceptual framework has, since everyone has a conceptual framework can break at any time and replaced by a ne

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Publication Date
Wed Jun 03 2020
Journal Name
Political Sciences Journal
The Muslim Arab Self and the image of the other, religiously and culturally different: a critical analytical study of the causes and forms of political and social intolerance in Iraq
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This research aims to analyze the intellectual and civilizational regression that afflicted Iraqi and Arab society due to political and religious tyranny and internal conflicts, which was reflected in the deterioration of human rights values and the absence of equality and justice in dealing with the other religiously, which affected the reluctance of members of religious groups to interact with their national societies and then migrate to Outside, which contributed to a double loss, in terms of the loss of these societies by productive and effective national competencies, and in terms of distorting the image of Islam. The research stressed that the first treatments of this phenomenon are the consolidation of the values of citize

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