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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 Jul 21 2018
Journal Name
The American Society For Virology's 38th Annual Meeting Will Be Held At The University Of Minnesota In Minneapolis, Mn
Comparative Study of different Predators’ effect on Chlorovirus Amplification Foraging on Zoochlorellae-Containing Paramecia?
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Publication Date
Sat Sep 01 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of risk management programs in Dealing With risks at international airports: An Applied research at Baghdad International Airport
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The objective of the research is to identify the efficiency of risk management in various names at Baghdad International Airport in the face of various risks (financial - technical - human - natural ..) facing the sample of the search of the General Establishment of Civil Aviation and the Iraqi Airways Company where the researcher identified the hypothesis that summarizes There is a significant significant correlation between risk management, risk management and risk review and assessment. The researcher used the means of research from observation and interviews with the relevant officials in this field, as well as used the questionnaire and distributed a sample of 170 employees in the field of risk management (SMS Department) in Iraqi A

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Publication Date
Tue Nov 09 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Adopting the green value chain to achieve sustainable competitive advantage: study to views of a sample from Ur General Company for Engineering Industries in Dhi Qar
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       In light of the developments and intense competition that the world has witnessed, the need to search for a sustainable and continuous competitive advantage for economic units has emerged, as the economic units must not lose sight of their interest in the activities they perform to achieve that advantage, and it can be said that the goal of the research is to identify the theoretical dimensions of the green value chain represented by: (Green research and development, green design, green manufacturing, green marketing, green services) and the dimensions of the sustainable competitive advantage represented by (quality, creativity, innovation, cost, response to the customer), as well as identifyi

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Publication Date
Mon Jun 01 2020
Journal Name
مجلة العلوم و التكنولوجية للنشاطات البدنية و الرياضية/ الجزائر
The effect of using the five-finger strategy on learning movement chain on a balance beam in the artistic gymnastics of women
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Abstract: The aim of the research identify the effect of using the five-finger strategy in learning a movement chain on the balance beam apparatus for students in the third stage in the College of Physical Education and Sports Science, as well as to identify which groups (experimental and controlling) are better in learning the kinematic chain on the balance beam device, has been used The experimental approach is to design the experimental and control groups with pre-and post-test. The research sample was represented by third-graders, as the third division (j) was chosen by lot to represent the experimental group, and a division Third (i) to represent the control group, after which (10) students from each division were tested by lot to repr

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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
ORGANIZATIONAL VALUES AND ITS IMPACT ON STRATEGIC PERFORMANCE A field study a comparison between Two Universities of Baghdad & Al-Nahrain
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ABSTRACT

     The researcher seeks to shed light on the relationship analysis and the impact between organizational values in all its dimensions (Administration Management, Mission, relationship management, environmental management) and strategic performance (financial perspective, customer perspective, the perspective of internal processes, learning and development) in the presidency of Two Universities of Baghdad & Al-Nahrain, it has been formulating three hypotheses for this purpose.

      The main research problem has been the following question: Is there a relationship and the impact of bet

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Publication Date
Fri Sep 01 2023
Journal Name
Migration Letters
Organizational Machiavellianism and Its Impact on Employees’ Passion: A Field Study on a Sample of Electronic Payment Companies in Iraq
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Publication Date
Fri Sep 30 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Evaluation of direct withholding tax procedures as a tool to increase tax proceeds : applied research in the General Tax Authority / Direct Deduction Department
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The research aims to evaluate the direct deduction department’s procedures for the process of collecting income tax using the direct deduction method for state departments and the public sector in light of direct deduction tax instructions No. (1) of 2007 and Income Tax Law No. (113) of 1982 (amended) through Giving a clear idea of ​​the reality of tax collection procedures because this type of tax is one of great importance because it contributes to the provision of financial revenues to the state to finance its expenses and direct the economy towards achieving its social, economic and political goals. The researcher makes comparisons between the procedures of the General Tax Authority in collecting the tax and what was approved b

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Publication Date
Sun Apr 01 2012
Journal Name
American Journal Of Applied Sciences
A New Strategy for Signaling Overhead Reduction in the Proxy Mobile IPv6 Protocol
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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of Planner And Development
Urban sustainability assessment for the urban renewal project in Al Shawaka a rea
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Sustainability is a major demand and need pursued by cities in all areas of life due to the environmental, social and economic gains they provide, especially in the field of city planning and urban renewal projects that aim to integrate the past, present and future.

 

The research aims to evaluate the Haifa Street renewal project, and Al-Shawaka district, one of the Baghdad districts located next to Al-Karkh, was elected by comparing the sustainability indicators of urban renewal with the reality of the situation through a field survey and questionnaire form and focusing on the social and economic impacts and environmental for the project on the study area. To reach the most important conclusions and recommendations

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Publication Date
Fri Nov 30 2018
Journal Name
Iop Conference Series: Materials Science And Engineering
Estimating the PVT Properties for Crude Oil from a Southern Iraqi Oil Field
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