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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
Sat Apr 10 2021
Journal Name
المؤتمر العلمي الدولي الثالث - المجلة الامريكية الدولية للعلوم الانسانية والاجتماعية
Public Governance and Sustainable Development - A descriptive study of the reality of public institutions in Iraq
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In light of crises, the need for efficient and flexible public administrations to make quick and decisive decisions, also institutions capable of directing the internal elements and components of them and adapting them to the requirements of rapid change due to crises and disasters, which led to scarce resources becoming scarcer and economic, political and social problems becomes more prominent. For the majority of developing countries, including Iraq, the increasing need for the importance of moving towards enhancing the efficiency of the performance of public institutions while trying to predict their future, can only be achieved. Through solid mechanisms and principles of governance that enhance the ability of institutions and make them

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Publication Date
Wed Jan 03 2024
Journal Name
Revista Brasileira De Engenharia Agrícola E Ambiental
Effect of cold plasma technique on the quality of stored fruits - A case study on apples
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The consumption of fresh fruits has increased nowadays due to the lifestyle of the consumers. Maintaining the quality and nutritional value of cut fruits during storage is difficult compared to whole fruits. Deterioration of internal and external quality usually occurs in freshly harvested fruits. It is necessary to use different techniques to maintain the quality and increase the shelf life of the freshly cut product. This research studied the effect of treating apple slices with cold plasma once and with filtered water again on quality characteristics (hardness, moisture content, sugar content, carbohydrate content, and color) after being stored for five days. The best treatment was determined using two different pressures of the plasma j

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Publication Date
Tue Nov 01 2016
Journal Name
International Journal Of Pharmaceutical Sciences Review And Research
A study on some variables affecting the preparation of ethyl cellulose based floating microspheres of lafutidine
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Lafutidine (LAF) a newly developed histamine H2-receptor antagonist with absorption window makes it a good candidate to be prepared as floating drug delivery system. The current study involves formulation and in- Vitro evaluation of lafutidine as floating microspheres. Different formulation variables that affect the physicochemical properties of the prepared microspheres besides to the drug release behavior were investigated. Fourteen formulas were prepared by emulsion (o/w) solvent evaporation method using Ethyl cellulose (EC) as the polymeric matrix and tween 80 (TW80) as an emulsifying agent. The prepared formulas were evaluated for their percentage buoyancy (%), Percentage yield (%) and Entrapment efficiency (EE %). The results obt

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Publication Date
Fri Mar 15 2019
Journal Name
Al-khwarizmi Engineering Journal
Experimental and Theoretical Study of the Energy Flow of a Two Stages Four Generators Adsorption Chiller
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This work is concerned with a two stages four beds adsorption chiller utilizing activated carbon-methanol adsorption pair that operates on six separated processes. The four beds that act as thermal compressors are powered by a low grade thermal energy in the form of hot water at a temperature range of 65 to 83 °C.  As well as, the water pumps and control cycle consume insignificant electrical power. This adsorption chiller consists of three water cycles. The first water cycle is the driven hot water cycle. The second cycle is the cold water cycle to cool the carbon, which adsorbs the methanol. Finally, the chilled water cycle that is used to overcome the building load. The theoretical results showed that average cycle cooling power

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Publication Date
Wed Jan 01 2025
Journal Name
Science Progress
Impact of COVID-19 on the prevalence of oral and maxillofacial disorders: A retrospective cohort study
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Publication Date
Tue Oct 01 2019
Journal Name
Ceramics International
A first-principles study of the electronic, structural, and optical properties of CrN and Mo:CrN clusters
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Publication Date
Sun Dec 12 2010
Journal Name
Journal Of Planner And Development
A documentary study of natural resources and ways of protecting them
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The problem of research is that there are ways to protect and sustain environmentally important sites in Iraq. There are no documentary sources for these sites, such as the natural landscape of natural and important natural resources, which suffer from severe environmental neglect

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Publication Date
Mon Nov 19 2018
Journal Name
Al–bahith Al–a'alami
A Proposed Vision for Editing News Forms
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This research deals with a very important subject as it tries to change the theoretical and scientific heritage and some professional rules adopted in the newsroom. Most media students have difficulties in writing news for press correctly. The researcher tries to identify the compatibility of what is published in local news agencies with professional and academic standards.
The research finds detailed editorial rules for a number of news formats which will play an important role in writing news for press easily, especially for the beginners and newcomers. Also, it discovers a new fact denying the beliefs of some researchers and writers in not having news conclusion in news edited according to the inverted pyramid pattern.
The re

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Publication Date
Sat Dec 03 2022
Journal Name
Tikrit Journal Of Pure Science
A Pixel Based Method for Image Compression
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The basic solution to overcome difficult issues related to huge size of digital images is to recruited image compression techniques to reduce images size for efficient storage and fast transmission. In this paper, a new scheme of pixel base technique is proposed for grayscale image compression that implicitly utilize hybrid techniques of spatial modelling base technique of minimum residual along with transformed technique of Discrete Wavelet Transform (DWT) that also impels mixed between lossless and lossy techniques to ensure highly performance in terms of compression ratio and quality. The proposed technique has been applied on a set of standard test images and the results obtained are significantly encourage compared with Joint P

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
A Proposed Agent System for Network Monitoring
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The traditional centralized network management approach presents severe efficiency and scalability limitations in large scale networks. The process of data collection and analysis typically involves huge transfers of management data to the manager which cause considerable network throughput and bottlenecks at the manager side. All these problems processed using the Agent technology as a solution to distribute the management functionality over the network elements. The proposed system consists of the server agent that is working together with clients agents to monitor the logging (off, on) of the clients computers and which user is working on it. file system watcher mechanism is used to indicate any change in files. The results were presente

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