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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
Fri Sep 01 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Assessing the Radiopacity of Three Resin Composite Materials Using a Digital Radiography Technique
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Background: Radiopacity is one of the prerequisites for dental materials, especially for composite restorations. It's essential for easy detection of secondary dental caries as well as observation of the radiographic interface between the materials and tooth structure. The aim of this study to assess the difference in radiopacity of different resin composites using a digital x-ray system. Materials and methods: Ten specimens (6mm diameter and 1mm thickness) of three types of composite resins (Evetric, Estelite Sigma Quick,and G-aenial) were fabricated using Teflon mold. The radiopacity was assessed using dental radiography equipment in combination with a phosphor plate digital system and a grey scale value aluminum step wedge with thickness

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Publication Date
Fri Sep 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Assessing The Radiopacity of Three Resin Composite Materials Using a Digital Radiography Technique
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Background: Radiopacity is one of the prerequisites for dental materials, especially for composite restorations. It's essential for easy detection of secondary dental caries as well as observation of the radiographic interface between the materials and tooth structure. The aim of this study to assess the difference in radiopacity of different resin composites using a digital x-ray system. Materials and methods: Ten specimens (6mm diameter and 1mm thickness) of three types of composite resins (Evetric, Estelite Sigma Quick,and G-aenial) were fabricated using Teflon mold. The radiopacity was assessed using dental radiography equipment in combination with a phosphor plate digital system and a grey scale value aluminum step wedge with thickness

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Publication Date
Mon Jan 01 2024
Journal Name
Polski Merkuriusz Lekarski
Design, synthesis, insilco study and biological evaluation of new isatin-sulfonamide derivatives by using mono amide linker as possible as histone deacetylase inhibitors
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Aim: To evaluate the cytotoxic activity of newly synthesized a series of novel HDAC inhibitors comprising sulfonamide as zinc binding group and Isatin derivatives as cap group joined by mono amide linker as required to act as HDAC inhibitors. Materials and Methods: The utilization of sulfonamide as zinc binding group joined by N-alkylation reaction with ethyl-bromo hexanoate as linker group that joined by amide reaction with Isatin derivatives as cap groups which known to possess antitumor activity in the designed of new histone deacetylase inhibitors and using the docking and MTT assay to evaluate the compounds. Results: Four compounds have been synthesized and characterized successfully by ART-FTIR, NMR and ESI-Ms. the compounds w

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Publication Date
Wed Dec 30 2020
Journal Name
Journal Of Planner And Development
Urban improvement, a mechanism of tourism development: Tébessa (Algeria) as a model
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The tourism industry has become, currently, an art, an industry and a science. It is also one of the components that make up touristic regions. Tourist attractions are no longer the exclusive visits of museums and archeological sites, but also involve other service facilities. It is, therefore, imperative that the authorities should become aware of the degradation of tourist resorts and prevent them from getting worse. Moreover, the authorities should take a set of decisions concerning the protection of the urban aspect with its historical, social, and environmental dimensions, as well as, adapting it to the modern requirements that can bring comfort to the citizens and tourists at physical and psychological levels.

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Publication Date
Fri Jul 21 2023
Journal Name
Journal Of Engineering
Shared Congestion Detection: A Comparative Study
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Most Internet-tomography problems such as shared congestion detection depend on network measurements. Usually, such measurements are carried out in multiple locations inside the network and relied on local clocks. These clocks usually skewed with time making these measurements unsynchronized and thereby degrading the performance of most techniques. Recently, shared congestion detection has become an important issue in many computer networked applications such as multimedia streaming and
peer-to-peer file sharing. One of the most powerful techniques that employed in literature is based on Discrete Wavelet Transform (DWT) with cross-correlation operation to determine the state of the congestion. Wavelet transform is used as a de-noisin

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Publication Date
Tue Dec 15 2020
Journal Name
Al-academy
Characteristics of Environment in Contemporary Iraqi and Iranian Pottery A Comparative Study (Saad Shakir- Muhammad Mahdi) A Model: قحطان عدنان محمود
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The Iraqi and Iranian pottery has a significant role in the contemporary world pottery space, despite the fact that influences created those formulation, thus the researcher supposes that there is a relation between the potter and his environment within Iraq's environment and Iran's environment, which are similar at times and different at other times. The researcher, hence, found himself in front of a number of questions:
1- How much was the Iraqi potter inspired by the environment compared to the Iranian potter?
2- Has the Iraqi and Iranian pottery been really inspired by the environment items or there were modified metaphors?
The current research aims at (identifying the influential environmental characteristics in the Iraq

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Publication Date
Sat Dec 01 2018
Journal Name
Al-khwarizmi Engineering Journal
A study of Land Zoning in the base of Traffic Noise Pollution Levels using ArcGIS: Kirkuk City as a Case Study
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This study is an approach to assign the land area of  Kirkuk city [ a city located in the northern of Iraq, 236 kilometers north of  Baghdad  and 83 kilometers  south of  Erbil [ Climatic atlas of  Iraq, 1941-1970  ]  into different  multi zones by using Satellite image and Arc Map10.3,  zones of different traffic noise pollutions. Land zonings process like what achieved in this paper will help and of it’s of a high interest point for the future of Kirkuk city especially urban

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Publication Date
Tue Aug 02 2022
Journal Name
Journal Of Legal Sciences
Expropriation of foreign investments - a comparative study
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The right to property is one of the most prominent and most important of the fundamental rights that the individual enjoys, whether national or foreign, both of them have their own private property that may not be affected except for the requirements of the country's economic development or what is known as the public benefit, and the Iraqi legislator did not specify what is meant by the removal of foreign investment. Of the bilateral international agreements (BITS), as it determined its terms and methods, the properties of foreign investors may be expropriated in a direct and indirect way.

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Publication Date
Tue Jan 09 2024
Journal Name
Wasit Journal Of Sports Sciences
A Comparative Analytical Study of Some Biomechanical Variables and Their Relationship to The Accuracy of The Performance of The Shooting Skill of Jumping High in The Weak and Strong Foot the Players for Youth Handball
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The research aims to identify the most important variables affecting shooting from jumping high and compare them for the two foot the weak and strong, where the researchers adopted the descriptive method, and the sample was chosen by the intentional method, which consists of (4) players from the Iraqi Sports Army Club, where these variables were studied and their impact on The accuracy of aiming at the two men, and the researchers concluded that most of the players have more accuracy in aiming at the strong leg than at the weak leg, which leads to the loss of many real opportunities during the match because of the players changing the situation or wasting the available opportunity when the position of correction is an opportunity for the w

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Publication Date
Wed Mar 15 2023
Journal Name
Al-academy
The gratifications of local television sports programs from the audience's point of view Analytical study for the period from 1/7/2022 to 01/10/2022
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The issue of sports media and its role in winning sports and non-sports fans and unifying them towards various issues and events is one of the important topics that have begun to occupy many countries and governments in the world and allocate appropriate spaces for it and provide it with sufficient funds and budgets to advance this reality...

Especially since the concept of the sports official has It changed a lot and turned into an economic concept rather than a sport one through the investment in the field of sports and the entry of capital and contributes to the prosperity of the countries interested in this field.

It is important that includes profit and loss in addition to knowing how to employ and win the masses and e

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