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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
Mon Dec 25 2017
Journal Name
Al-khwarizmi Engineering Journal
A new Cumulative Damage Model for Fatigue Life Prediction under Shot Peening Treatment
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 Abstract

In this paper, fatigue damage accumulation were studied using many methods i.e.Corton-Dalon (CD),Corton-Dalon-Marsh(CDM), new non-linear model and experimental method. The prediction of fatigue lifetimes based on the two classical methods, Corton-Dalon (CD)andCorton-Dalon-Marsh (CDM), are uneconomic and non-conservative respectively. However satisfactory predictions were obtained by applying the proposed non-linear model (present model) for medium carbon steel compared with experimental work. Many shortcomings of the two classical methods are related to their inability to take into account the surface treatment effect as shot peening. It is clear that the new model shows that a much better and cons

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Publication Date
Sun Dec 01 2024
Journal Name
Al-kindy College Medical Journal
A Revolutionary Road Map for Obesity Management and Beyond: Tirzepatide as a Dual-Acting Insulinotropic Polypeptide Receptor Agonist
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Tirzepatide is a revolutionary and promising medication with a high impact in the treatment of Obesity and T2DM with their complications. Its efficacy was proven through different trials in achieving favorable weight loss and a significant reduction in glycemic index. It also treated a large diversity of related co-morbidities, including fatty liver, cardiovascular disease, dyslipidemia, and more. Tirzepatide is well tolerated, has a good safety profile, and is highly reliable and suitable for use in a population.

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Publication Date
Sat Jun 25 2022
Journal Name
International Journal Of Drug Delivery Technology
Assessment of Serum Levels of the WNT Pathway Antagonist (Dickkopf-1) in a Sample of Type 2 Diabetic Patients with Retinopathy using Two Groups of Antidiabetics
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Objectives: Dickkopf-1 (DKK-1) is WNT/b-catenin pathway antagonist which plays a detrimental role in the development of diabetic retinopathy (DR). This research aimed to assess serum DKK-1 levels in diabetic patients who have and have not developed DR and, compare them with the control subjects finding out whether we can use it as an indicator for DR early diagnosis and to find out which one of the widely used two groups of antidiabetic treatments had the greater effect on this biomarker and hence on the progression of DR. Methods: The study participants were divided into two subgroups: First, 70 patients (36 male, 34 female) with type 2 diabetes mellitus, among them 35 patients diagnosed with DR and 35 with no evidence of DR, and s

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Publication Date
Sat Mar 31 2018
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Study of the Performance of Paraffin Wax as a Phase Change Material in Packed Bed Thermal Energy Storage System
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The present work deals with an experimental investigation of charging and discharging processes in thermal storage system using a phase change material PCM. Paraffin wax was used as the PCM which is formed in spherical capsules and packed in a cylindrical packed column which acted as an energy storage system. Air was used as the heat transfer fluid HTF in thermal storage unit. The effect of flow rate and inlet temperature of HTF on the time of charging and discharging process were studied. The results showed that the faster storage of thermal energy can be made by high flow rate of heat transfer fluid HTF and high inlet temperature of heat transfer fluid. It was found that at 65°C HTF inlet temperature, the melting and solidification pr

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Publication Date
Tue Dec 30 2014
Journal Name
College Of Islamic Sciences
Social solidarity in religions        Three / critical study
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The researcher wanted to make an attempt to identify the foundations of social solidarity, to strengthen the bonds of brotherhood among society, and spread the causes of compassion in the hearts of its members.
       The researcher has taken a short course in the hearts of the beloved to hearts.

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The research is based on a thesis not discussed: Test the strategy of the General Organization based on the model Wichler and Bakov A case study at the Iraqi Ministry of Interior
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The study aimed at identifying the strategic gaps in the actual reality of the management of public organizations investigated to determine the strategy used based on the study model. The study relied on the variable of the general organization strategy in its dimensions (the general organization strategy, the organization's political strategy and the defense strategy of the organization) The sample of the study was (General Directorate of Traffic, Civil Status Directorate and Civil Defense Directorate), formations affiliated to the Ministry of the Interior, for the importance of the activity carried out by these public organizations by providing them In order to translate the answers into a quantitative expression in the analysi

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Publication Date
Mon Oct 01 2018
Journal Name
Al–bahith Al–a'alami
Axiology of Electronic programs in updating the methodology of information and communication sciences Tropes 8.4 Case Study
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The study aims to display the scientific benefit offered by modern electronic programs for various scientific research methods, while determining the positive scientific role played by these programs in modernizing the methodologies and logic of scientific thinking, especially with the rapid development of the sciences and their curricula.
These programs link accurately with scientific results. The importance of the study is to provide practical mechanisms to highlight the scientific projection of the electronic programs in various steps of scientific research.
A case study was used for Tropes version 8.4, which analyzes written, audio and visual semantic texts and presents a set of statistical results that facilitate the difficult

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
A study of fermi hole for some atomic systems
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the electron correlation effect for inter-shell can be described by evaluating the fermi hole and partial fermi hole for Li atom comparing with Be+ and B+2 ions

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Publication Date
Fri Aug 01 2014
Journal Name
Int. J. Mod. Eng. Res
Exact solutions for MHD flow of a viscoelastic fluid with the fractional Burgers’ model in an annular pipe
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This paper presents an analytical study for the magnetohydrodynamic (MHD) flow of a generalized Burgers’ fluid in an annular pipe. Closed from solutions for velocity is obtained by using finite Hankel transform and discrete Laplace transform of the sequential fractional derivatives. Finally, the figures are plotted to show the effects of different parameters on the velocity profile.

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Publication Date
Thu Apr 06 2023
Journal Name
International Journal Of Emerging Technologies In Learning (ijet)
The Impact of a Scenario-Based Learning Model in Mathematics Achievement and Mental Motivation for High School Students
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