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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
Sun Feb 23 2020
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
The philosophy of the workplace spirituality in the third millennium organizations: A field study at the Ministry of Health Center
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Publication Date
Wed Apr 01 2020
Journal Name
Isa Transactions
Design of a Complex fractional Order PID controller for a First Order Plus Time Delay system
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Publication Date
Wed Jun 01 2022
Journal Name
Analytical Methods In Environmental Chemistry Journal
Design a continuous microfluidic flow cell for turbidimetric-flow injection technology: A new approach for routine analysis of active pharmaceutical formulations
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Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The effects of human error in the banking risks - Empirical study in a number of Iraqi private banks
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Abstract

This research aims to study human error effects in the banking risks in the private banks  through the measurement and testing of human error effect in every kind of banking risks types and stand on the most closely associated with the risks in order to focus on them and make appropriate processors have with respect to and increase the availability of skills and expertise required to carry out banking operations of error-free manner.

Find dealt with human error in terms of meaning and understandable, classifications and types, causes and consequences and its approaches and theories. Also addressed placed banking risks in terms of meaning and concept, species and entr

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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
A Statistical Study of the Amount of Radiation Generated from Communication Towers in the Nineveh Plain Region, Baghdeda
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This research presents a statistical study of radiation generated from communication towers in the Nineveh Plain region Baghdeda. The intensity of radiation energy was measured at 10 meters away from the communication tower in different locations, using a (1PC XH-901 Dosimeter/ Personal Dose Alarm / Radiation Detector, dosage rate: 0.01 μSv/h to 150μSv/h) to measure the amount of radiation at various times. Energy densities were measured and compared with standard limits provided by other authorities, such as the International Committee for Radiation Protection. Results were analyzed using SPSS version 26 to implement the data. The results show that the means of the radiation levels measured at all the zones do not statistically differ

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Publication Date
Fri Jul 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Productive role in the financial performance of the banking: An Empirical Study in a sample of Iraqi banks
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The research aims to study the basic concepts of banking productivity and discuss different approaches to study what ends to identify the most important possible standards applied to measured within the Iraqi banking environment as well as research into the causes of low and high Iraqi banking productivity and identify possible treatments to curb those reasons as to ensure the rise. And in line with the research problem, which states what is the level of productivity and what are the causes of decline and the rise in private banking research sample individually. And what the Iraqi private banks and what is the relationship between performance and the impact of productivity change in the perform

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Publication Date
Mon Dec 03 2018
Journal Name
Journal Of Engineering
Comparative Analysis of Various Multicarrier Modulation Techniques for Different Multilevel Converters
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The applications of Multilevel Converter (MLC) are increased because of the huge demand for clean power; especially these types of converters are compatible with the renewable energy sources. In addition, these new types of converters have the capability of high voltage and high power operation. A Nine-level converter in three modes of implementation; Diode Clamped-MLC (DC-MLC), Capacitor Clamped-MLC (CC-MLC), and the Modular Structured-MLC (MS-MLC) are analyzed and simulated in this paper. Various types of Multicarrier Modulation Techniques (MMTs) (Level shifted (LS), and Phase shifted (PS)) are used for operating the proposed Nine level - MLCs. Matlab/Simulink environment is used for the simulation, extracting, and ana

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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
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
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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