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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 May 01 2022
Journal Name
Journal Of Engineering
The Collapsible Soil, Types, Mechanism, and identification: A Review Study
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Collapsible soil has a metastable structure that experiences a large reduction in volume or collapse when wetting. The characteristics of collapsible soil contribute to different problems for infrastructures constructed on its such as cracks and excessive settlement found in buildings, railways channels, bridges, and roads. This paper aims to provide an art review on collapse soil behavior all over the world, type of collapse soil, identification of collapse potential, and factors that affect collapsibility soil. As urban grow in several parts of the world, the collapsible soil will have more get to the water. As a result, there will be an increase in the number of wetting collapse problems, so it's very important to com

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Publication Date
Wed Mar 30 2022
Journal Name
Gsc Biological And Pharmaceutical Sciences
Using the silicon (luminal cast plastination technique) for the lower respiratory tract in sheep as an alternative to cement
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The lower respiratory tract of sheep was studied to determine the torsion and branching of the bronchial tree. The respiratory system of ruminants and all living organisms is one of the most important organs in the body that controls the amount of gas exchange between the heart and lungs through the airways, it is clear that in sheep it consists of a narrow bronchial tube that reaches the extent of lung tissue repercussions. He used silicon, water, acid, and at room temperature, and the substance was injected with an injection gun through the trachea and was pushed gently to spread and distribute in all parts of the lungs with moderate manual pressure. The results showed that the mold shape in the lung and the bronchial branches of

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
measure the relationship between imported inflation and foreign trade in the Iraqi economy for long 1990-2015 using model nardl
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The study aims to discuss the relation between imported inflation and international trade of Iraqi economy for the period (1990-2015) by using annual data. To achieve the study aim, statistical and Econometrics methods are used through NARDL model to explain non-linear relation because it’s a model assigned to measure non-linear relations and as we know most economic relations are non-linear, beside explaining positive and negative effects of imported inflation, and to reach the research aim deductive approach was adopted through using descriptive method to describe and determine phenomenon. Beside the inductive approach by g statistical and standard tools to get the standard model explains the

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Publication Date
Sat May 01 2010
Journal Name
Journal Of Baghdad College Of Dentistry
Comparison of microleakage Restorative Dentistry Comparison of microleakage in three different retrograde cavity preparations with Mineral Trioxide Aggregate as filling material
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Background: The apical seal is the single most important factor in determining the success of surgical endodontics, the aim of this study was to compare the sealing ability of Mineral Trioxide Aggregate in three different cavity designs. Materials and Methods: Thirty extracted human single-rooted teeth were divided into three groups of ten teeth per group, a retrograde cavity preparation was carried out using a low speed handpiece and round bur with parallel walls in the first group, ultrasonic retrotip and unit in the second group and a low speed handpiece with a carbide inverted cone bur with undercuts in the third group, all the cavities were filled with MTA. microleakage was measured by dye penetration technique using methylene blue. Re

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Molecular diagnosis of E.coliO157:H7 Which Isolated from Children with Diarrhea by using Multiplex PCR
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A total of 96 stool samples were collected from children with bloody diarrhea from two hospitals in Baghdad. All samples were surveyed and examined for the presence of the Escherichia coli O157:H7 and differentiate it from other Non -Sorbitol Fermenting Escherichia coli (NSF E. coli). The Bacterial isolates were identifed by using morphological diagnostic methods, Samples were cultured on liquid enrichment medium, incubated at 37C? for 24 hrs, and then cultured on Cefixime Tellurite -Sorbitol MacConkey Agar (CT- SMAC). 32 non-sorbitol fermenting bacterial isolates were obtained of which 11 were identified as Escherichia coli by using traditional biochemical tests and API20E diagnostic system without differentiation between

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Publication Date
Thu Jun 30 2022
Journal Name
Iraqi Journal Of Laser
PDF Towards C+L Band Three-Mode (De)Multiplexer Using Subwavelength Grating (SWG) Technology
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Abstract: Recently, there is increasing interest in using mode-division multipelexing (MDM) technique  to enhace  data rate transmission over multimode fibers.  In this technique, each fiber mode is treated as a separate optical carrier to transfer its own data.  This paper presents a broadband, compact, and low loss three-mode (de)multiplexer designed for C+L band using subwavelength grating (SWG) technology and built-in silicon-on-insulator SOI platform. SWG offers refractive index engineering for wider operating bandwidth and compact devices compared to conventional ones. The designed (de)multiplex deals with three modes (TE0, TE1, and TE2) and has a loss > -1 dB and crosstalk < −15 dB, and its operation c

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Publication Date
Sat Dec 31 2022
Journal Name
International Journal Of Intelligent Engineering And Systems
Using Three-Dimensional Logistic Equations and Glowworm Swarm Optimization Algorithm to Generate S-Box
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Publication Date
Thu Jun 01 2023
Journal Name
International Journal Of Agricultural And Statistical Sciences
Forecasting the Saudi Crude Oil Price Using MS-GARCH Model
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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Estimate the Partial Linear Model Using Wavelet and Kernel Smoothers
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This article aims to estimate the partially linear model by using two methods, which are the Wavelet and Kernel Smoothers. Simulation experiments are used to study the small sample behavior depending on different functions, sample sizes, and variances. Results explained that the wavelet smoother is the best depending on the mean average squares error criterion for all cases that used.

 

 

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Publication Date
Thu Sep 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
The Role of Product Innovation on an Improvement of the Organization's Reputation /A Field Study in State Organization for Marketing of Oil (SOMO)
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 This paper aims to verify the existence of relationships between product innovation and the reputation of the organization. The study problem is that the State Organization for Marketing of Oil (SOMO) system is inflexible in terms of marketing procedures and needs innovative, unconventional methods in innovating its products and improving performance. The reputation of the organization. The importance of the study lies in that it is an attempt to raise the interest of SOMO in its approach to the research variables in order to enhance its competitive position in the future and improve the marketing business environment, which contributes to enhancing the reputation of the organization by product innovation. The study sample

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