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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
Mon Oct 03 2022
Journal Name
International Journal Of Interactive Mobile Technologies (ijim)
A New Feature-Based Method for Similarity Measurement under the Linux Operating System
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This paper presents a new algorithm in an important research field which is the semantic word similarity estimation. A new feature-based algorithm is proposed for measuring the word semantic similarity for the Arabic language. It is a highly systematic language where its words exhibit elegant and rigorous logic. The score of sematic similarity between two Arabic words is calculated as a function of their common and total taxonomical features. An Arabic knowledge source is employed for extracting the taxonomical features as a set of all concepts that subsumed the concepts containing the compared words. The previously developed Arabic word benchmark datasets are used for optimizing and evaluating the proposed algorithm. In this paper,

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Publication Date
Wed Mar 01 2023
Journal Name
Journal Of Engineering
Recycled Concrete Aggregated for the use in Roller Compacted Concrete: A Literature Review
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The using of recycled aggregates from construction and demolition waste (CDW) can preserve natural aggregate resources, reduce the demand for landfill, and contribute to a sustainable built environment. Concrete demolition waste has been proven to be an excellent source of aggregates for new concrete production. At a technical, economic, and environmental level, roller compacted concrete (RCC) applications benefit various civil construction projects. Roller Compacted Concrete (RCC) is a homogenous mixture that is best described as a zero-slump concrete placed with compacting equipment, uses in storage areas, dams, and most often as a basis for rigid pavements. The mix must be sufficiently dry to support

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Publication Date
Sat Jan 25 2025
Journal Name
Al-mansour Journal
The Multi-Period Probabilistic Inventory Model Applied at the General Company for Leather Industries
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In this research, the multi-period probabilistic inventory model will be applied to the stores of raw materials used in the leather industry at the General Company for Leather Industries. The raw materials are:Natural leather includes cowhide, whether imported or local, buffalo leather, lamb leather, goat skin, chamois (raw materials made from natural leather), polished leather (raw materials made from natural leather), artificial leather (skai), supplements which include: (cuffs - Clocks - hands - pockets), and threads.This model was built after testing and determining the distribution of demand during the supply period (waiting period) for each material and completely independently from the rest of the materials, as none of the above mate

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Publication Date
Sun Jul 02 2006
Journal Name
Journal Of The Faculty Of Medicine Baghdad
a placebo control study of the effect of nigella sativa fixed oil on the healing rate of recurrent aphthous ulceration
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Publication Date
Fri Jun 16 2023
Journal Name
Journal Of Humanities And Social Sciences Researches
The Role and Importance of Electronic Automation in Banking Service Development: A Case Study of the Commercial Bank of Iraq
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Electronic banking services appeared as a result of laying the foundations for the application of electronic automation in the banking field, and despite the clear expansion in its adoption and implementation as an inevitable necessity imposed by international and national developments, its application was not ideal according to the level that was expected to occur after the abandonment of traditional banking services, which produced some risks Which is evident in the absence of a legal system, whether at the level of proving and authoritative electronic banking services such as electronic signature, Or at the level of protecting the confidentiality of these services and ensuring that they are not exp

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Publication Date
Tue Oct 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
The applicability of green productivity tools: An analytical study in a sample of industrial companies in the province of Nineveh
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                The current research aims to identify the most important green productivity tools GPT and the possibility of applied in industrial companies in general and the companies operating in the province of Nineveh, in particular, as well as the study of some personality characteristics and functional, which is believed to be an impact on the application of these tools in industrial companies. Accordingly, the research community of managers in the company of medicines and medical supplies ready-made clothes _ operating in the province of Nineveh, who are (80) while the manager was subjected to research procedures (49) Director representing (61.25%)

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Publication Date
Thu Jul 18 2024
Journal Name
Journal Of Economics And Administrative Sciences
The Role Of Cognitive Sharing In Enhancing The E-Learning Quality An Analytical Study Of A Sample Of Iraqi Universities
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The world faced many communication challenges in 2020 after the Covid-19 pandemic, the most important of which was the continuation of schooling. Therefore, the research aimed to analyze the current reality of the studied universities in terms of strengths and weaknesses and measure the implementing level of quality requirements of e-learning. This research studies the impact of knowledge sharing in its dimensions (behavior, organizational culture, work teams, and technology) on the e-learning quality and its dimensions (e-learning management, educational content, evaluation ,and evaluation). After conducting the survey, there was a difference in the universities’ application of the quality requirements of e-learning, as the study

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Publication Date
Sun Jan 13 2019
Journal Name
Iraqi Journal Of Physics
A Study of the effect of adding antimony oxide to the coating surfaces of steel and cast Iron by glass
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The study included adding antimony oxide to mixtures of coating metal surfaces (Enameling), after it was selected ceramic materials used in the coating metal pieces of the type of steel and cast iron in two layers. The first is called a ground coat and the second is a cover coat.
Ceramic materials layer for ground coat have been melted down in
platinum crucible at a temperature of 1200oC to prepare the glass
mixture (Frit). It was coated on metals at a temperature of 780oC for
two minutes, while the second layer was prepared glass mixture
(Frit) at a temperature of 1200oC, but was coated at a temperature of
760oC for two minutes.
Underwent tests crystalline state of powders (Frits) and enameled samples using X-ray di

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Impact of Envy on Workplace Stress A field Study of Faculty Staff at the Technical College of Management-Baghdad
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The research aims to measure the impact of envy on job stress because the topic of envy represents a negative emotion that exists at all organizational levels, which may cause stress in the work environment.

The Research problem is represented by the lack of perception of most of the faculty staff on the negative effects of envy on their well-being in the Technical College of Management - Baghdad, and what is the impact level of envy on their job stress.

To achieve this, the scale of envy was based on two dimensions (being envied, Envying others), While the job stress scale was based on seven dimensions (workload, conflict role, Family factors, work environment, work relationships

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Publication Date
Sat Jan 01 2011
Journal Name
Journal Of Engineering
Simulation Model for the Assessment of Direct and Indirect Georeferencing Techniques in Analytical Photogrammetry
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B Saleem, H Alwan, L Khalid, Journal of Engineering, 2011 - Cited by 2

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