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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 Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Entry cost based on activity-based cost specifications and comparative study
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Several recent approaches focused on the developing of traditional systems to measure the costs to meet the new environmental requirements, including Attributes Based Costing (ABCII). It is method of accounting is based on measuring the costs according to the Attributes that the product is designed on this basis and according to achievement levels of all the Attribute of the product attributes. This research provides the knowledge foundations of this approach and its role in the market-oriented compared to the Activity based costing as shown in steps to be followed to apply for this Approach. The research problem in the attempt to reach the most accurate Approach in the measurement of the cost of products from th

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Publication Date
Thu Sep 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Dental Aerosol Hazard Prevention with Pre-procedural Antiseptic Mouthwashes (Comparative Study)
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Background: One of the recommended methods for reducing aerosol contamination during the daily regular usage of high-speed turbine and ultrasonic scaling is the use of preprocedural mouth rinse. Several agents have been investigated as a preprocedural mouth rinse. Chlorhexidine significantly reduce the viable microbial content of aerosol when used as a preprocedural rinse. Studies have shown that cetylpridinum chloride (CPC) mouthwash is equally effective as chlorhexidine in reducing plaque and gingivitis. This study compared the effect of 0.07% CPC to 0.2% chlorhexidine gluconate (CHX) as preprocedural mouth rinses in reducing the aerosol contamination by high-speed turbine. Materials and Methods: 36 patients were divided into three gro

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Publication Date
Sun Mar 02 2008
Journal Name
Baghdad Science Journal
Three-Dimensional Microfabrication With Conjugated Polymers
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In this paper we reported the microfabrication of three-dimensional structures using two-photon polymerization (2PP) in a mixture of MEH-PPV and an acrylic resin. Femtosecond laser operating at 800nm was employed for the two-photon polymerization processes. As a first step in this project we obtained the better composition in order to fabricate microstructers of MEH-PPV in the resin via two-photon polymerzation. Acknowledgement:This research is support by Mazur Group, Harvrad Universirt.

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Publication Date
Mon Dec 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The effect of promotion means in the developing the activity of financial markets: A case study of Iraqi stock Exchange
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The promotion by its means lead a vital and important role at the level of all organizations, whether (industrial or service) in general, and financial markets in particular. The promotion is earns delved to be as one of the main operations which  market uses it through various means of financial markets and companies which its shares listed in the aim of (finance or investment), with a view to the implementation and financing of public and private projects the one hand, or with a view to achieving profits through investment of speculative or... For other purposes, on the other hand.Accordingly, we find that the set of public and private goals joint between the financial markets and listed companies respectively, will serve the stra

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
A study of the physical and chemical characteristics of the waters of the central marshes in southern Iraq after restoration
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some ecological (physical and chemical varible) of water samples were studies monthly from December 2008 to May 2009 at two stations( St.1) Al - Chibayesh marsh and (St.2) Abu – Zirik marsh which are located in the south of Iraq . These variables included : Temperature, pH, EC, Dissolved oxygen , Total alkalinity, Nitrate, Sulphate, and phosphate, Si-SiO2 and Ca ,Mg, Cl, The marsh Considered as fresh water and alkaline. Abu-Zirik less than Al-Chibayesh.

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Publication Date
Fri Sep 30 2022
Journal Name
College Of Islamic Sciences
The Effectiveness of Combining the Meanings of Grammatical Tools in Understanding the Arabic Sentence A study of Some Linguistic Evidences
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abstract

The grammatical tools (the letters of meanings) are of great importance in understanding the meanings of the Arabic sentences,

This research is a simple attempt to show how our venerable scholars employed the meanings of these tools when they interpreted the linguistic evidence, that is, the grammatical structure largely depends on the tool in forming the meaning within the sentences and employing the meanings of these grammatical tools in explaining the linguistic evidence by clarifying their significance in the contexts of their use and effectiveness. Synthesis of the meanings of grammatical tools is an important tool in understanding the linguistic structure in order to reveal its meaning.

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Publication Date
Thu Jan 16 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Security and confidentiality of information and its impact on the competitive performance of insurance companies: A prospective study for the Iraq insurance company and ALhamraa Insurance company (private)
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The security of information represent the available  protection of  information and its component and guaranty the its safety and confidentiality. The absent or lack or stop of security of information and without maximum benefit may lead to lose confidence and make it burden on the company. So we must protect the company and information from the damages which may lead to the frailer of performance and loses of the company and its workers. So the security of information considered one of the potential  and controlling basis to protect individuals and companies from the damages. To insure the security  and confidentiality of information there are delicate,  proper and trusted ways, like FIRE WALL, PASS WORD, SYPHAR

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Publication Date
Tue Sep 30 2014
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Analytical Model for Detection the Tilt in Originally Oil Water Contacts
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Many carbonate reservoirs in the world show a tilted in originally oil-water contact (OOWC) which requires a special consideration in the selection of the capillary pressure curves and an understanding of reservoir fluids distribution while initializing the reservoir simulation models.
An analytical model for predicting the capillary pressure across the interface that separates two immiscible fluids was derived from reservoir pressure transient analysis. The model reflected the entire interaction between the reservoir-aquifer fluids and rock properties measured under downhole reservoir conditions.
This model retained the natural coupling of oil reservoirs with the aquifer zone and treated them as an explicit-region composite system

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Publication Date
Mon Jan 01 2024
Journal Name
Lecture Notes In Networks And Systems
Using Machine Learning to Control Congestion in SDN: A Review
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Publication Date
Tue Feb 20 2024
Journal Name
Baghdad Science Journal
A New Strategy to Modify Hopfield by Using XOR Operation
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The Hopfield network is one of the easiest types, and its architecture is such that each neuron in the network connects to the other, thus called a fully connected neural network. In addition, this type is considered auto-associative memory, because the network returns the pattern immediately upon recognition, this network has many limitations, including memory capacity, discrepancy, orthogonally between patterns, weight symmetry, and local minimum. This paper proposes a new strategy for designing Hopfield based on XOR operation; A new strategy is proposed to solve these limitations by suggesting a new algorithm in the Hopfield network design, this strategy will increase the performance of Hopfield by modifying the architecture of t

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