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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 Jan 13 2016
Journal Name
University Of Baghdad
Employ Mathematical Model and Neural Networks for Determining Rate Environmental Contamination
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Publication Date
Fri Mar 01 2024
Journal Name
Advances In Structural Engineering
Simulation and design model for reinforced concrete slabs with lacing systems
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Lacing reinforcement plays a critical role in the design and performance of reinforced concrete (RC) slabs by distributing the applied loads more evenly across the slab, ensuring that no specific area of the slab is overloaded. In this study, nine slabs, divided into three groups according to the investigated parameters, were meticulously designed and evaluated to study the interplay between the lacing reinforcement and other key parameters. Each slab was crafted for simple support and was subjected to both static and repeated two-point load tests. The lacing reinforcement had an angle of 45° with various tension and lacing steel. The repeated-tested specimens with lacing reinforcement experienced smaller ductility than those of s

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Publication Date
Fri Mar 01 2024
Journal Name
Advances In Structural Engineering
Simulation and design model for reinforced concrete slabs with lacing systems
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Lacing reinforcement plays a critical role in the design and performance of reinforced concrete (RC) slabs by distributing the applied loads more evenly across the slab, ensuring that no specific area of the slab is overloaded. In this study, nine slabs, divided into three groups according to the investigated parameters, were meticulously designed and evaluated to study the interplay between the lacing reinforcement and other key parameters. Each slab was crafted for simple support and was subjected to both static and repeated two-point load tests. The lacing reinforcement had an angle of 45° with various tension and lacing steel. The repeated-tested specimens with lacing reinforcement experienced smaller ductility than those of s

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Publication Date
Thu Jan 10 2019
Journal Name
Journal Of The College Of Education For Women
Tribal separation and its relation to the organization of the community from the point of view of tribal sheikhs Field study in the City of Baghdad Sadr City model))
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One of topics that occupied alarge area  in Iraqi  society  at the moment is the  issue( of tribal  separation and its  relation  to the organization of  the community ) so we see in the civilizations and heritage  of each community aset  of provisions and laws that take the form of status   customary or religious it is indicative of the great interest in Iraqi society in cotrolling the behavior of individuals to comply with values and social laws and become their behavior is consistent with the behavior of the total and adhere to the social values and be productive individuals within  the subject and this can only be  achieved  from the social co

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Publication Date
Wed Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
Forced displacement in Iraq its causes and its effects on displaced families (A field study of displaced families to the city of Baghdad)
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After a temporary halt to forced thghebr in different cities of Iraq this methodlogy
opeations returned directiy in the areas of political conflict on the ground which are translated
operations and forced displacement violence es they operations aimed at completing the
forced displacement that occurred after the occupation in(2003)which took an upward curve
publicly after these events and some of which are aimed at the liquidation of some provinces
than any demographic diversity of religious or sectarian or alhens and others aimed at
redemographic distribution within the province itself to produce a net sectarian zones as is the
case in Diyala Nineveh and Babylon Baghdad has the epicenter of sectarian violence and th

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Publication Date
Sun Apr 30 2023
Journal Name
Al-kindy College Medical Journal
Influence of Vitamin D Deficiency on the Level of Salivary cathelicidin LL-37 in relation to Dental Caries Experience: A Case-Control Study
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Background: Vitamin D improves innate immunity by enhancing the expression of antimicrobial peptides. The antimicrobial action of cathelicidin is widespread and effective against cariogenic bacteria. This research aimed to investigate the effect of vitamin D deficiency on the level of salivary cathelicidin concerning dental caries experience.

Subjects and Methods: A case-control study was carried out, and the sample was composed of 80 females; the study group involved 40 females with a serum vitamin D concentration of less than 10 ng/ml. In addition to the control group involving 40 females wh

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Publication Date
Tue Jan 19 2021
Journal Name
Isprs International Journal Of Geo-information
The Potential of LiDAR and UAV-Photogrammetric Data Analysis to Interpret Archaeological Sites: A Case Study of Chun Castle in South-West England
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With the increasing demands to use remote sensing approaches, such as aerial photography, satellite imagery, and LiDAR in archaeological applications, there is still a limited number of studies assessing the differences between remote sensing methods in extracting new archaeological finds. Therefore, this work aims to critically compare two types of fine-scale remotely sensed data: LiDAR and an Unmanned Aerial Vehicle (UAV) derived Structure from Motion (SfM) photogrammetry. To achieve this, aerial imagery and airborne LiDAR datasets of Chun Castle were acquired, processed, analyzed, and interpreted. Chun Castle is one of the most remarkable ancient sites in Cornwall County (Southwest England) that had not been surveyed and explored

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Publication Date
Mon Mar 09 2026
Journal Name
Al–bahith Al–a'alami
The Impact of Means of Communication on Electoral Behavior and its Relationship to the Political Disparity of the Family (A Field Study of an Audience of the University of Baghdad’s Students)
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Iraq has seen many changes at the social, economic and political levels. This led to cause many shifts in the structure of its society and imposed great challenges reflected in the behavior and awareness of that society in general and youth in particular.

Those changes made the Iraqi society undergoing the transformation of value and culture aspects formed a political awareness that caused cultural and political diversity within the family and society. A greater openness to the outside world caused by the communication revolution, as the world has witnessed during the past two decades, has helped in making that change. Iraq had its share of media and political openness, which were included after the US occupation in 2003. As a re

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Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Extent of Organizational Dynamic Capabilities' Contribution to Human Talent Management: An Analytical Study of the Opinions of a Sample of Administrative Leaders in the Presidency of the University of Mosul.
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Actual and effective organizational dynamic capabilities in the work environment contribute to a number of factors that contribute to the organization's ability to manage its human talents. Thus, the study sought to identify the level of contribution of organizational dynamic capabilities to human talent management based on their dimensions in the investigated organization by determining the level of relationship and impact between these variables. The presidency of Mosul University was chosen as a field for the current study, and data were collected by adopting the questionnaire form as the main tool for the study. The study used a deliberate sample of (42)  administrative leaders in the investigated organization and adopte

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Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Extent of Organizational Dynamic Capabilities' Contribution to Human Talent Management: An Analytical Study of the Opinions of a Sample of Administrative Leaders in the Presidency of the University of Mosul.
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The recognition of the dynamic organizational capabilities in their actual and influential extent in the work environment achieves a set of positive data that can fall under the addition axes, particularly with regard to the organization's ability to manage human talents in them, so the researchers sought to identify the level of contribution of dynamic organizational capabilities in the management of human talents in terms of Keep them away in the research organization by indicating the level of relationship and impact between them. The presidency of Mosul University was chosen as a field for the current study, and data were collected by adopting the questionnaire form as the main tool for the study. The study used a deliberate

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