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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 10 2019
Journal Name
Iraqi Journal Of Physics
A study of the effect of acid immersion on some physical properties of ( Epoxy – MgO) composites
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In this study a polymeric composite material was prepared by hand
lay-up technique from epoxy resin as a matrix and magnesium oxide
(MgO) as a reinforcement with different weight fraction (5,10,15,
and 20)% to resin. Then the prepared samples were immersed under
normal condition in H2So4(1 M) solution, for periods ranging up to
10 weeks. The result revealed that the diffusion coefficient
decreasing as the concentration of MgO increase. Also we studied
Hardness for the prepared samples before and after immersion. The
result revealed that the hardness values increase as the concentration
of MgO increase, while the hardness for the samples after immersion
in H2SO4 dec

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Publication Date
Sun May 28 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
On-Line Navigational Problem of a Mobile Robot Using Genetic Algorithm
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Publication Date
Thu Jul 01 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A proposed encryption technique of different texts using circular link lists
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Publication Date
Wed Aug 12 2020
Journal Name
International Journal On Advanced Science, Engineering And Information Technology
Developing of a 3D Printer to Produce Parts Using Powder Metal
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Publication Date
Thu Mar 09 2023
Journal Name
Coatings
Nondestructive Evaluation of Fiber-Reinforced Polymer Using Microwave Techniques: A Review
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Carbon-fiber-reinforced polymer (CFRP) is widely acknowledged as a leading advanced material structure, offering superior properties compared to traditional materials, and has found diverse applications in several industrial sectors, such as that of automobiles, aircrafts, and power plants. However, the production of CFRP composites is prone to fabrication problems, leading to structural defects arising from cycling and aging processes. Identifying these defects at an early stage is crucial to prevent service issues that could result in catastrophic failures. Hence, routine inspection and maintenance are crucial to prevent system collapse. To achieve this objective, conventional nondestructive testing (NDT) methods are utilized to i

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Publication Date
Sun Dec 30 2012
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Removal of Nickel Ions Using A Biosorbent Bed (Laminaria saccharina) Algae
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The present study aims to remove nickel ions from solution of the simulated wastewater using (Laminaria saccharina) algae as a biosorbent material. Effects of experimental parameters such as temperature at (20 - 40) C⁰, pH at (3 - 7) at time (10 - 120) min on the removal efficiency were studied.
Box-Wilson method was adopted to obtain a relationship between the above three experimental parameters and removal percentage of the nickel ions. The experimental data were fitted to second order polynomial model, and the optimum conditions for the removal process of nickel ions were obtained.
The highest removal percentage of nickel ions obtained was 98.8 %, at best operating conditions (Temperature 35 C⁰, pH 5 and Time 10 min).

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Publication Date
Thu Oct 31 2019
Journal Name
Al-kindy College Medical Journal
Using Zinc in Management of Subfertile Male Patients: a Clinical Trial
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Background: The use of minerals in treatment of different diseases is as old as man himself. zinc is the most famous trace mineral related to male sexual function. Oligoasthenozoospermic subfertile patients were treated with zinc sulphate for three months.

Objectives: Aim of the research is to investigate the role of Zinc and if it affects the abnormalities of some semen parameters and to study the possible role of pharmaceutical preperations of zinc in amelioration of male subfertility as well as to assess the ability of Zinc to induce changes in the serum and semen zinc levels in addition to the levels of reproductive hormones (FSH and Testosterone).

Type of the study:

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Publication Date
Fri Mar 31 2017
Journal Name
Journal Of Engineering
Aerodynamic Characteristics of a Rectangular Wing Using Non-LinearVortex Ring Method
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The aerodynamic characteristics of general three-dimensional rectangular wings are considered using non-linear interaction between two-dimensional viscous-inviscid panel method and vortex ring method. The potential flow of a two-dimensional airfoil by the pioneering Hess & Smith method was used with viscous laminar, transition and turbulent boundary layer to solve flow about complex configuration of airfoils including stalling effect. Viterna method was used to extend the aerodynamic characteristics of the specified airfoil to high angles of attacks. A modified vortex ring method was used to find the circulation values along span wise direction of the wing and then interacted with sectional circulation obtained by Kutta-Joukowsky the

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Publication Date
Sun Apr 30 2017
Journal Name
Journal Of Engineering
Implementation of a Proposed Load-Shedding System Using Altera DE2 FPGA
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A load-shedding controller suitable for small to medium size loads is designed and implemented based on preprogrammed priorities and power consumption for individual loads. The main controller decides if a particular load can be switched ON or not according to the amount of available power generation, load consumption and loads priorities. When themaximum allowed power consumption is reached and the user want to deliver power to additional load, the controller will decide if this particular load should be denied receiving power if its priority is low. Otherwise, it can be granted to receive power if its priority is high and in this case lower priority loads are automatically switched OFF in order not to overload the power generation. The

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Suggested Model for auditing the performance of municipal institutions to verify the services provided
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The services provided by the municipal institutions of the basic things needed by the man in his daily life and the evolution of cities basically depends on these services and therefore has paid most of the world's attention to this vital facility and give him the biggest concern for the welfare of the citizens, as is the research problem that there is no program scrutiny to evaluate the performance of municipal institutions contribute to measuring the efficiency and effectiveness of the services provided and was based on research on the premise that the preparation of the existence of audit program to evaluate the performance of municipal institutions contribute to measuring the efficiency and effectiveness of services provided has reac

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