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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
Thu Oct 01 2020
Journal Name
Journal Of Engineering
Chemical-Free Greywater Treatment Using Aeration, Sedimentation, Followed by Granular Activated Carbon Filter (GAC) -A Case Study of Baghdad city household
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Greywater is a possible water source that can be improved for meeting the quality required for irrigation. Treatment of greywater can range from uncomplicated coarse filtration to advanced biological treatment. This article presents a simple design of a small scale greywater treatment plant, which is a series of physical and natural processes including screening, aeration, sedimentation, and filtration using granular activated carbon filter and differentiates its performance with sand filter. The performance of these units with the dual filter media of (activated carbon with sand) in treatment of greywater from Iraqi house in Baghdad city during 2019 and that collected from several points including washbasins, kitchen si

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Publication Date
Sun Jan 01 2012
Journal Name
Iraqi Journal Of Science
REMOTE SENSING MONITORING OF CHANGES IN SOIL POLLUTION A CASE STUDY IN A REGION IN BAGHDAD, IRAQ
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One of the main environmental problems which affect extensively the areas in the world is soil salinity. Traditional data collection methods are neither enough for considering this important environmental problem nor accurate for soil studies. Remote sensing data could overcome most of these problems. Although satellite images are commonly used for these studies, however there are still needs to find the best calibration between the data and real situations in each specified area. Landsat satellite (TM & ETM+) images have been analyzed to study soil pollution (Exacerbation of salinity in the soil without the use of abandoned agricultural for a long time) at west of Baghdad city of Iraqi country for the years 1990, 2001 & 2007. All of the th

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Publication Date
Tue Jun 30 2020
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
RATIONALIZATION OF CONSUMPTION AND ITS IMPACT ON ECONOMIC DEVELOPMENT (A PRELIMINARY STUDY): RATIONALIZATION OF CONSUMPTION AND ITS IMPACT ON ECONOMIC DEVELOPMENT (A PRELIMINARY STUDY)
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The research deals with the concept of rationalization of consumption, which is legitimately legitimized, by indicating the permissibility of consumption and its limits in Islam, the legitimate aspects of spending and its controls, and the concept of development in the Islamic economy. The researcher followed the descriptive method by presenting the legal texts and jurisprudential opinions and linking them to contemporary economic problems.The research has reached several conclusions, the most important of which is that the goal of Islam in relation to consumption is to inform the Muslim of the amount of economic maturity, and the truth of alms is good in money and religion. It is necessary for achieving maturity that both means

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Publication Date
Tue Feb 03 2026
Journal Name
Al–bahith Al–a'alami
The Role of Media Coverage of the Iraqi Satellite Channels in Shaping Public Attitudes towards Terrorism (a Field Study of a Sample of an Audience of the City of Baghdad)
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Violence is one of the most serious threats facing societies because it affects their internal structure and threatens the security and stability of society. It is classified as one of the types of security crises that are emerging in Arab and Islamic societies in particular, and in most countries of the world in general.

The threat of this crisis is increasing. Terrorism is considered as one of the most serious aspects of that all the countries of the world, currently, suffer from. The terrorism has begun to penetrate deep into society in one way or another starting from the Second World War, which led to the emergence of leftist movements in Western Europe, Japan, France, Italy and other countries as a result of emerging ideas

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Publication Date
Sun Mar 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Spectral fluctuations in <sup>24</sup>Mg nucleus using the framework of the nuclear shell model
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Abstract<p>Random matrix theory is used to study the chaotic properties in nuclear energy spectrum of the <sup>24</sup>Mg nucleus. The excitation energies (which are the main object of this study) are obtained via performing shell model calculations using the OXBASH computer code together with an effective interaction of Wildenthal (W) in the isospin formalism. The <sup>24</sup>Mg nucleus is assumed to have an inert <sup>16</sup>O core with 8 nucleons (4protons and 4neutrons) move in the 1d<sub>5/2</sub>, 2s<sub>1/2</sub> and 1d<sub>3/2</sub> orbitals. The spectral fluctuations are studied by two statistical measures: the nearest neighb</p> ... Show More
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Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Relationship between Fiscal Policy and Human Development Analytical Studay Of Iraq Using The (ARDL)Model
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Fiscal policy is one of the important economic tools that affect economic development in general and human development in particular through its tools (public revenues, public expenditures, and the general budget).

It was hoped that the effects of fiscal policy during the study period (2004-2007) will positively reflect on human development indicators (health, education, income) by raising these indicators on the ground. After 2003, public revenues in Iraq increased due to increased revenues. However, despite this increase in public budgets, the actual impact on human development and its indicators was not equivalent to this increase in financial revenues. QR The value of the general budget allocations ha

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Publication Date
Sun Dec 31 2023
Journal Name
Nativa,
Benthic invertebrate at three sites on the Tigris River, Iraq
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The study was conducted from November 2021 to May 2022 at the three study sites within the Baghdad governorate. The study aims to identify the impact of human activities on the Tigris River, so an area free of human activities was chosen and represented the first site. A total of 48 types were diagnosed, 6204 ind/m3 spread over three sites. The following environmental indicators were evaluated: Constancy Index (S), Relative abundance index (Ra), Richness Index (between 17.995 and 23.251), Shannon Weiner Index (0.48-1.25 bit/ind.), Uniformity Index (0.124 -0.323). The study showed that the highest percentage recorded was for the phylum Annileda 34%; and the stability index shows that taxes (Stylaria sp., Aoelosoma sp., Branchinra sowerby, Ch

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Publication Date
Thu Jan 01 2015
Journal Name
Journal Of Engineering
A Visual Interface Design for Evaluating the Quality of Google Map Data for some Engineering Applications
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Today, there are large amounts of geospatial data available on the web such as Google Map (GM), OpenStreetMap (OSM), Flickr service, Wikimapia and others. All of these services called open source geospatial data. Geospatial data from different sources often has variable accuracy due to different data collection methods; therefore data accuracy may not meet the user requirement in varying organization. This paper aims to develop a tool to assess the quality of GM data by comparing it with formal data such as spatial data from Mayoralty of Baghdad (MB). This tool developed by Visual Basic language, and validated on two different study areas in Baghdad / Iraq (Al-Karada and Al- Kadhumiyah). The positional accuracy was asses

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Publication Date
Thu Jan 30 2020
Journal Name
Journal Of Engineering
  Positional Accuracy Assessment for Updating Authoritative Geospatial Datasets Based on Open Source Data and Remotely Sensed Images
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OpenStreetMap (OSM) represents the most common example of online volunteered mapping applications. Most of these platforms are open source spatial data collected by non-experts volunteers using different data collection methods. OSM project aims to provide a free digital map for all the world. The heterogeneity in data collection methods made OSM project databases accuracy is unreliable and must be dealt with caution for any engineering application. This study aims to assess the horizontal positional accuracy of three spatial data sources are OSM road network database, high-resolution Satellite Image (SI), and high-resolution Aerial Photo (AP) of Baghdad city with respect to an analogue formal road network dataset obtain

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Publication Date
Wed Mar 23 2022
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a Training Program for the Development of Moral Intelligence among Preparatory Students
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This current research aims to identify the effectiveness of a training program in developing moral intelligence and mutual social confidence among middle school students. The researcher made a number of hypotheses for this purpose to achieve the goal of the research.                             

The researcher relied on the (Al Zawaida 2011) scale prepared according to Coles (1997), including (60) items, and the mutual social trust scale for (Nazmi 2001) based on Roter's theory including (38) items.               &nbsp

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