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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 Apr 14 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Study The Effect of α-amylase Inhibitors Isolated from Plant Sources on Some Mold.: Study The Effect of α-amylase Inhibitors Isolated from Plant Sources on Some Mold.
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Activity test of the inhibitors purified from barley and broad beans crop proved the inhibition activity against 6 types of rots Pencillium ssp and Aspergellusflavus and Aspergillus niger and Fusarium solani and Fusarium semitectum and Mucor with three concentrations 0.1 and 0.2 and 0.3 mg/ml, where the inhibitor purified from the second peak of broad beans proved that it had a higher inhibition activity against the growth of test rots which were 53.75 and 62.5 and 78.5 and 76.25 and 84 and 18.8% respectively, at 0.3 mg/ ml followed by the first peak of the inhibitor purified from broad beans the inhibition activity were 43.75 and 50 and 62.96 and 75 and 80 and 12.5 then the inhibitor purified from barley in which the inhibition activity

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Publication Date
Mon Dec 03 2018
Journal Name
Journal Of Engineering
Similarity and Difference between Sustainable and Green Architecture (a Comparative Study)
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The research is concerned with studying the characteristics of Sustainable Architecture and Green Architecture, as a general research methodology related to the specific field of architecture, based on the differentiation between two generic concepts, Sustainability and Greening, to form the framework of the research specific methodology, where both concepts seem to be extremely overlapping for research centers, individuals, and relevant organizations. In this regard, the research tend towards searching their characteristics and to clearly differentiates between the two terms, particularly in architecture, where the research seeks understanding sustainable and green architectures, how they are so close or so far, and the

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Publication Date
Tue Apr 02 2024
Journal Name
Journal Of Engineering
Revolutionizing Depth Sensing: A Review Study of Apple LiDAR Sensor for as-built Scanning Applications
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Incorporating the LiDAR sensor in the most recent Apple devices represents a substantial development in 3D mapping technology. Meanwhile, Apple's Lidar is still a new sensor. Therefore, this article reviews the potential uses of the Apple Lidar sensor in various fields, including engineering and construction, focusing on indoor and outdoor as-built 3D mapping and cultural heritage conservation. The affordable cost and shorter observation times compared to traditional surveying and other remote sensing techniques make the Apple Lidar an attractive choice among scholars and professionals. This article highlights the need for continued research on the Apple LiDAR sensor technology while discussing its specifications and limitations. A

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Publication Date
Fri Nov 05 2021
Journal Name
Review Of International Geographical Education Online
Measuring The Efficiency of The Departments of The College of Administration and Economics / University of Baghdad Using the Method of Data Envelopment Analysis (DEA), A Comparative Study
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Publication Date
Fri Jan 01 2021
Journal Name
Review Of International Geographical Education Online
Measuring The Efficiency of The Departments of The College of Administration and Economics / University of Baghdad Using the Method of Data Envelopment Analysis (DEA), A Comparative Study
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The research aims at the possibility of measuring the technical and scale efficiency (SE) of the departments of the College of Administration and Economics at the University of Baghdad for a period lasting 8 years, from the academic year 2013-2014 to 2018-2019 using the method of Applied Data Analysis with an input and output orientation to maintain the distinguished competitive position and try to identify weaknesses in performance and address them. Nevertheless, the research problem lies in diagnosing the most acceptable specializations in the labor market and determining the reasons for students’ reluctance to enter some departments. Furthermore, the (Win4DEAp) program was used to measure technical and scale efficiency (SE) and rely on

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Publication Date
Sun Jun 01 2025
Journal Name
Irish Journal Of Medical Science (1971 -)
Enhanced diagnostic accuracy of type 1 diabetes mellitus through the combined use of serum β-catenin and HbA1c
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Publication Date
Mon Apr 01 2019
Journal Name
Journal Of Educational And Psychological Researches
Psychological and Health Risks of Children Toy-Related Injuries: Pellet-Gun as a Model
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The research aims to identify the psychological and health risks that a child might be exposed to by playing with hazardous toys such as pellet guns. To this end, the researcher has visited Ibn Al-Haytham Eye Hospital in Baghdad, the emergency department to figure out the rate of injuries in Children for the consecutive years (2017-2018) and the first Month of (2019). The psychological risks as a result of disability are represented by the inability to accommodate the surrounding environment well. Additionally, the child experiences a kind of tension, conflict, and going in psychological crises through introversion, isolation, withdrawal tendencies, and poor conformity with himself and the Society.

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Publication Date
Wed Feb 05 2020
Journal Name
Political Sciences Journal
Frustrations of sectarian coexistence and mechanisms to activate peaceful coexistence: Iraq as a model
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Abstract The study aimed at demonstrating the reality of sectarian coexistence in Iraq, which was characterized by the tolerance and coercion caused by the successive government policies to govern Iraq and to this day. The study was based on the hypothesis that coexistence between Islamic sects in Iraq can be achieved as long as there are strong bonds linking its components, and these bonds can produce coexistence between the sects based on peace. The study concluded that the hypothesis is correct, in addition to drawing a set of observations aimed at identifying weaknesses for advancing them through the adoption of mechanisms that address these weaknesses to yield towards a genuine peaceful coexistence among Islamic sects in Iraq.

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Publication Date
Wed Jul 31 2019
Journal Name
Journal Of Engineering
Evaluation of the Accuracy of Digital Elevation Model Produced from Different Open Source Data
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This study aims to estimate the accuracy of digital elevation models (DEM) which are created with exploitation of open source Google Earth data and comparing with the widely available DEM datasets, Shuttle Radar Topography Mission (SRTM), version 3, and Advanced Spaceborne Thermal Emission and Reflection Radiometer Global Digital Elevation Model (ASTER GDEM), version 2. The GPS technique is used in this study to produce digital elevation raster with a high level of accuracy, as reference raster, compared to the DEM datasets. Baghdad University, Al Jadriya campus, is selected as a study area. Besides, 151 reference points were created within the study area to evaluate the results based on the values of RMS.Furthermore, th

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Publication Date
Sun Dec 02 2018
Journal Name
Journal Of The College Of Education For Women
Poverty and its Relations to Some Social Variables (Children in the Primary Stage as a Model)
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The phenomenon of poverty is one of the most important phenomena facing the world at large. Despite the tremendous technological progress witnessed by mankind and despite the unprecedented high levels of world economic production, poverty remains the greatest challenge facing the world. Statistics and studies have shown that poverty is caused by several problems: (health, social, economic, educational, etc.) These problems are obstacles to the ability to obtain employment opportunities, which leads in the beginning to the growth phenomenon of unemployment, and ultimately to the growth of poverty.

The results of a range of research in the field of psychology have confirmed that children from poor homes suffer from a high level of

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