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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
Tue Jan 01 2019
Journal Name
Journal Of Theoretical And Applied Information Technology
A Survey on the Vein Biometric Recognition Systems: Trends and Challenges
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Vascular patterns were seen to be a probable identification characteristic of the biometric system. Since then, many studies have investigated and proposed different techniques which exploited this feature and used it for the identification and verification purposes. The conventional biometric features like the iris, fingerprints and face recognition have been thoroughly investigated, however, during the past few years, finger vein patterns have been recognized as a reliable biometric feature. This study discusses the application of the vein biometric system. Though the vein pattern can be a very appealing topic of research, there are many challenges in this field and some improvements need to be carried out. Here, the researchers reviewed

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Publication Date
Sun Apr 08 2018
Journal Name
Al-khwarizmi Engineering Journal
Building a Management System to Control the Construction Claims in Iraq
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The paper deals with claims in construction projects in Iraq and studies their types, causes, impacts, resolution methods and then proposes a management system to control the impacts of claims. Two parts have been done to achieve the research objective (theoretical part and practical part). The findings showed that the main types of the claims are extra work claims, different site condition claims, delay claims and the main causes of the claims are variation of the orders, design errors and omission, delay in payments by owner, variation in quantities and scheduling errors. The claims have bad impacts on the cost by increasing (10% to 25%) and also on the duration of the project by increasing from (25% to 50%).The negotiation is the main

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Publication Date
Tue Aug 01 2023
Journal Name
Journal Of Engineering
Developing a Proposed System to Organize the Investment Opportunities in Iraq
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The Iraqi government seeks to overcome the financial crisis by investing and privatizing some projects to achieve sustainable growth. Most of the investment projects in Iraq suffer from many constraints that greatly impact the success of these projects. A survey of the opinions of a group of experts was conducted to identify the most important constraints facing the investment process in Iraq. Then the experts' answers were arranged in a closed questionnaire and distributed to the research sample for which the statistical analysis was conducted. Through it, the most important (17) factors that had the greatest impact on the failure of investment projects in Iraq were reached. One of the main constraints was

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Publication Date
Sun May 17 2026
Journal Name
Journal Of The College Of Education
A New Text from Ur III dynasty on Ba’aga, the fattener
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يعد هذا النص أحد النصوص المسمارية المصادرة التي بحوزة المتحف العراقي، ويحمل الرقم المتحفي (235869)، قياساته )12،7x 6x 2،5سم). يتضمن مدخولات كميات من الشعير،أرخ النص الى عصر أور الثالثة (2012-2004 ق.م) و يعود الى السنة الثالثة من حكم الملك أبي-سين (2028-2004 ق.م)،أن الشخصية الرئيسة في هذا النص هو)با-اَ-كا مسمن الماشية( من مدينة أري-ساكرك، ومقارنته مع النصوص المسمارية المنشورة التي تعود الى أرشيفه يبلغ عددها (196) نصاً تضمنت نشاطاته م

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Publication Date
Wed May 14 2025
Journal Name
Reproductive Biology And Endocrinology
The aryl hydrocarbon receptor: a new frontier in male reproductive system
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Background: The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor historically recognized for its role in the regulation of toxicity mediated by environmental chemicals. Recent research points to AhR's critical participation in male reproductive physiology, particularly in spermatogenesis, hormone signaling, and the maintenance of sperm quality. Both endogenous ligands (e.g., dietary and gut microbiota-derived metabolites) and exogenous pollutants (e.g., dioxins and benzo-α-pyrene) influence AhR-mediated pathways, making it a key link between environmental exposures and male fertility. Results: This review highlights AhR's influence on the male reproductive system, emphasizing the role of endogenous AhR ligands an

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Publication Date
Thu Jul 07 2022
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
COMPARISON BETEEEN THE CONSUMPTION OF RED MEAT AND WHITE MEAT FOR ASAMPLE OF CITIZENS OF THE CITY OF BAGHDAD/ AN EXPLORATORY STUDY : COMPARISON BETEEEN THE CONSUMPTION OF RED MEAT AND WHITE MEAT FOR ASAMPLE OF CITIZENS OF THE CITY OF BAGHDAD/ AN EXPLORATORY STUDY
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Three hundred Iraqi people participated in demographic and attitudes study about red and white meat consumption. The mean age of the participants was 50 SD ± 11 years (mean 30-72); 51% were females and 49% males, mostly in forties who lived ≥ 5 years in Baghdad. The results showed that 80% of individuals prefer red meat. A 90% of people prefer fresh meat compared to frozen and processed meat. A 60% of people buy meat from popular markets. Nearly 87% of respondents believe the improving of livestock sector is essential and 80% of people confirmed there are obstacles to development this sector. An 80% of participates thought the reasons of the high prices of local fresh meat is the lack of plann

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Publication Date
Sat Feb 01 2020
Journal Name
Journal Of Southwest Jiaotong University
The Dynamics of an Eco-Epidemiological Model with Allee Effect and Harvesting in the Predator
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The aim of this study was to propose and evaluate an eco-epidemiological model with Allee effect and nonlinear harvesting in predators. It was assumed that there is an SI-type of disease in prey, and only portion of the prey would be attacked by the predator due to the fleeing of the remainder of the prey to a safe area. It was also assumed that the predator consumed the prey according to modified Holling type-II functional response. All possible equilibrium points were determined, and the local and global stabilities were investigated. The possibility of occurrence of local bifurcation was also studied. Numerical simulation was used to further evaluate the global dynamics and the effects of varying parameters on the asymptotic behavior of

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Publication Date
Sun Apr 01 2018
Journal Name
Journal Of Educational And Psychological Researches
The effectiveness of Barman model in acquiring the historical concepts among fourth-grade literary students
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The researcher attempts to examine Barman model in acquiring the historical concepts among fourth-grade students at literary classrooms. To this end, the researcher held the null hypothesis, there is no significant difference between the experimental groups who was taught based on Barman model and the control group that taught based on the traditional method in acquiring the historical concepts on the post-test. To testify the effectiveness of Barman model, the researcher administered a questionnaire included (60) items on bunch of female-students who were selected from al-khamaeal preparatory school in al-hurriyah district in Baghdad. The author utilized different statistical tools to analyze the collected data.    &

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Publication Date
Sun Jul 01 2018
Journal Name
Journal Of Educational And Psychological Researches
The effectiveness of Barman model in acquiring the historical concepts among fourth-grade literary students
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The researcher attempts to examine Barman model in acquiring the historical concepts among fourth-grade students at literary classrooms. To this end, the researcher held the null hypothesis, there is no significant difference between the experimental groups who was taught based on Barman model and the control group that taught based on the traditional method in acquiring the historical concepts on the post-test. To testify the effectiveness of Barman model, the researcher administered a questionnaire included (60) items on bunch of female-students who were selected from al-khamaeal preparatory school in al-hurriyah district in Baghdad. The author utilized different statistical tools to analyze the collected data.    &

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Publication Date
Tue Jan 11 2022
Journal Name
3rd International Scientific Conference Of Alkafeel University (iscku 2021)
Elimination of the broadening in X-ray diffraction lines profile for nanoparticles by using the analysis of diffraction lines method
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In this research, the results of the Integral breadth method were used to analyze the X-ray lines to determine the crystallite size and lattice strain of the zirconium oxide nanoparticles and the value of the crystal size was equal to (8.2nm) and the lattice strain (0.001955), and then the results were compared with three other methods, which are the Scherer and Scherer dynamical diffraction theory and two formulas of the Scherer and Wilson method.the results were as followsScherer crystallite size(7.4nm)and lattice strain(0.011968),Schererdynamic method crystallite size(7.5 nm),Scherrer and Wilson methodcrystallite size( 8.5nm) and lattice strain( 0.001919).And using another formula for Schearer and Wilson methodwe obtain the size of the c

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