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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
Tue Jan 01 2019
Journal Name
Energy Procedia
Calculating Surface Roughness for a Large Scale SEM Images by Mean of Image Processing
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Publication Date
Mon Sep 01 2014
Journal Name
19th International Conference On Methods And Models In Automation And Robotics (mmar) 2014
A PSO-optimized type-2 fuzzy logic controller for navigation of multiple mobile robots
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Publication Date
Sun Oct 01 2017
Journal Name
Ieee Transactions On Neural Systems And Rehabilitation Engineering
A Framework of Temporal-Spatial Descriptors-Based Feature Extraction for Improved Myoelectric Pattern Recognition
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Publication Date
Wed Jun 07 2023
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a Program in Developing Awareness of the Criteria for Judging Electronic Educational Materials Among Students of Teaching Diploma at Dhofar University
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The study aims to develop the awareness of the criteria for judging electronic educational materials among students of educational qualification at Dhofar University over spreading the Corona pandemic through a program based on mini-educational units. The study was applied to (18) students studying Teaching diploma at Dhofar University for the academic year 2020-2021, and their number. They were chosen intentionally. The study resulted in reaching a list of criteria for judging electronic educational materials, roughly (18) criteria in the selection themes and (15) criteria in the use theme. The level of awareness of the sample members with the criteria for selecting and using electronic educational materials and the effectiveness of the

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Publication Date
Mon Feb 18 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Role of Insurance Awareness in marketing Insurance Services: An Explorative Research views of a Sample of Employees in the National Company for Insurance
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This research aims at shedding light on the concept of insurance awareness and clarifying its role on marketing insurance services of a sample of (100) employees in the National Company for Insurance. Questionnaire is used as a main instrument for collecting data and information from the sample. Their answers were analyzed by using arithmetic means, standard deviation, centesimal weight, and the correlation coefficient ( , F, t) tests .The research reached several conclusions of which:1.The sample member's response to insurance awareness and marketing insurance services factors was in the medium level.2.There was a positive relationship of a moral sign between insurance awareness and marketing insurance services, that correlation coeffic

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Publication Date
Sun Sep 01 2013
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The contractual budget: the ideal technique in planning and implementing capital budgeting projects: a strategy of preparing the contractual budget for Baghdad local government
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Public budget is the government's tool in achieving the objectives of economic and social development is the accounting curriculum to estimate state revenues and expenditures for years to come, as well as to have legal status as it is after the adoption of an official statement of government units to spend funds on items planned at the same time is a statement collect resources to finance these appropriations, if the primary objective of the budget initially limited to the achievement of financial and legislative control have evolved this function in the area of public administration turned attention from mere imposition of control over the money, which provides information to assist the Department to utilize available resources and prog

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Publication Date
Sat Dec 28 2024
Journal Name
Journal Of College Of Physical Education
Design and standardization of a progressively difficult educational test for football passing skills for first-year students in the College of Physical Education and Sports Sciences
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Standards play a vital role in documenting the values ​​of new test results in the form of tables. They are one of the basic requirements that the standardization process aims for as a complement to standardizing test procedures, and contribute to knowing the current reality of the student. The degree of readiness and level as a result of practicing different exercises for sports activities, in addition to the possibility of adopting it for comparison with his group or similar groups, classification, prediction and selection. Developing the skill of handling the football in the educational field is an important matter for achieving distinguished performance among students. This skill requires a level of accuracy, speed and control, and

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Publication Date
Fri Jul 28 2023
Journal Name
Journal Of Optics
Estimated the nanoparticles size of CdS from UV–Vis spectrum absorption by effective mass approximation model (EMA) using capping and complex agent
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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Using Regression Analysis as Analytical Procedure to Facilitate the Decision-Making Process in The Tax Audit: An Applied Research in the General Commission of Taxes
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This research aims to clarify the advantages of using the regression method as analytical procedure in the tax audit to reducing the examination cost , time, effort, human and material resources, and represents an applied study in the General Commission of taxes. In order to achieve its objectives the research has used in the theoretical side the descriptive approach (analytical), and in the practical side regression method has been applied to the research sample represented by the soft drinks company that is subject to the tax settlement for the year 2014, where the value of sales has been verified by using the regression method without conductinga comprehensive examination. The most important results of the research indicate that the r

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Publication Date
Tue Aug 03 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The impact of tax techniques on the quality of services provided to income taxpayers: An exploratory study in a sample of the branches of the General Tax Authority / Baghdad Governorate
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The research aims to demonstrate the impact of tax techniques on the quality of services provided to income taxpayers by studying the correlational and influencing relationships between the exploited variable (tax techniques) and the dependent variable (the quality of services provided to income taxpayers), and in line with the research objectives, the main hypothesis of the research was formulated (there is a relationship Significance between tax techniques and the quality of services provided to income taxpayers) a number of sub-hypotheses emerged from this hypothesis that were stated in the research methodology, and a number of conclusions were reached, the most important of which were (through the use of the correlation coeff

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