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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 Jun 21 2021
Journal Name
International Medical Journal
Immediate and Delay Antimicrobial Activity of Three Disinfection Solutions on Gutta-Percha Cones as Routine Chair-Side Procedure
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Objective: The antimicrobial efficacy of three disinfection solutions: 5.25% sodium hypochlorite (NaOCl), 2% chlorhexidine (CHX) and Listerine mouthwash were investigated as routine chair-side gutta-percha (GP) disinfection reagents. Design: four groups of gutta percha points were contaminated with E. faecalis bacteria then disinfected by immersion in different solutions (5.25% sodium hypochlorite, 2% chlorhexidine gluconate, Listerine mouth wash and distilled water as control) after 1 and 7 days culturing periods. The antibacterial efficacy of these disinfection solutions was evaluated by using colonies per units (CPU) Methods: Forty GP cones (F3 Dentsply) were sterilized with ethylene oxide gas before immersed contamination within broth m

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Publication Date
Fri Mar 25 2022
Journal Name
Asian Journal Of Biochemistry, Genetics And Molecular Biology
Evaluation of the Simple Sequence Repeats to Work as a Phase Variation with the Neisseria meningitidis Genome
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Background: The most crucial mechanism of genetic variation in N. meningitidis is the slipped strand mispairing, this mechanism generates Phase variation using simple sequence repeat (SSR) and is commonly used by the N. meningitidis to escape the immune system despite its function in eradicating the pathogenic and commensal bacteria. Some of simple sequence repeats (SSRs) that located within the genome works as phase variation while other SSRs have no role in generating phase variation mechanisms. Therefore, Aim: the main goal of the current in silico study was to detect the probability of SSR to enroll with phase variation for the entire N. meningitidis genome. Methods: Different criteria were used to judge SSR as

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Publication Date
Mon Jan 02 2017
Journal Name
Al-academy
The semiology of culture and the sign variable in a theatre performance: Iraqi theatre as an example
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The culture of theatre performance has a vital role in the process of reading the linguistic and visual signs of the performance. And the process of transforming a theatre performance from its original context into a new hosting cultural context starts from the actual reading of the text. Directors derives their new signs out of his personal culture, depending on the society where they lives and the culture that forms the social conventions, traditions and beliefs. The text is usually written within its own historical and temporal culture. The process of its production usually takes it away from its original culture, when it interprets the codes of the original writer and their visual and linguistic signs and instils new alternative sign

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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
Political finance: a study on the financing of political parties
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 Parties as active units in this process in order to work must have access to sources of funding in order to maintain their political presence in society and participate in the process of electoral competition, To win the election, bolstering the huge role that money has played in influencing the principle of equality among contestants in the elections. Those who own money will have a greater chance of winning the elections while less competitive opportunities for others who do not own the money or what they own does not give them the competitive ability to win elections. From this point of view, controlling political finance through legal regulation and institutional, media and popular monitoring has become an important requirement

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Publication Date
Fri Jul 01 2022
Journal Name
Iop Conference Series: Earth And Environmental Science
A study Some Technical Indicators of the Local Designed Machine
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Abstract<p>The effect of compound machine on wheat/ AlNoor cultivar was studied based on some technical indicators. were tested under three speeds ( 2.541, 3.433 and 4.091km.hr<sup>-1</sup>) and three tillage depths (14, 16 and 18cm). The experiments were conducted in a factorial experiment under complete randomized design with three replications. The results showed that the 2.541km.hr<sup>-1</sup> practical speed was significantly better than other two speed in all studied conditions. Except for the FC, which achieved the best results with the third speed 4.091 km.hr<sup>-1</sup>. mechanical parameters, plant growth parameters and yield and growth parameters. The 1</p> ... Show More
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Publication Date
Thu Sep 30 2021
Journal Name
International Journal Of Research In Social Sciences And Humanities
The Anonymous Identity of Forced Migrants: A Post-Colonial Study
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Colonialism invades the Third World countries, physically and psychologically. This article exposes but sample of the physical and psychological consequences of colonialism. The Beekeeper of Aleppo (2019) by the British novelist, Christy Lefteri is a typical novel to diagnose the harsh circumstances of individuals within and after the disaster. Since it depicts characters from Asian countries, it would be a best representative for all Asian people who suffer colonialism. Migration toward anonymity is the mere option for the colonized people. Aftermath, they experience displacement, trauma, and the loss of identity.

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Publication Date
Fri Nov 21 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A study to compare the cleaning efficiency of different irrigation systems for macro debris removal in instrumented canals (An in vitro study)
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Background: Irrigation of the canal system permits removal of residual tissue in the canal anatomy that cannot be reached by instrumentation of the main canals so the aim of this study was to compare and evaluate the efficiency of conventional irrigation system, endoactivator sonic irrigation system,P5 Newtron Satelec passive ultrasonic irrigation and Endovac irrigation system in removing of dentin debris at three levels of root canals and to compare the percentage of dentin debris among the three levels for each irrigation system. Materials and methods: Forty extracted premolars with approximately straight single root canals were randomly distributed into 4 tested groups of 10 teeth each. All canals were prepared with Protaper Universal ha

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
The regulatory climate in the government and private kindergarten children (Comparative Study)
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The research problem boils question is there in Riyadh organizational climate that enables them to do their work properly and whether there are differences between the government and private Riyadh depending on the organizational climate has sought Find measure: 1 regulatory climate for kindergarten 2. The difference between government and private Riyadh depending on the organizational climate. Limited research on the (200) parameter of the Riyadh government and private parameters for the year (20,142,015) In order to achieve the research objectives the researchers built a regulatory climate in accordance with the scientific steps to build a psychological scales measure After the formulation of climate regulation paragraphs of the (30) p

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Publication Date
Wed Jan 01 2020
Journal Name
Transplantation Proceedings
Outcomes of SGLT2 Inhibitors Use in Diabetic Renal Transplant Patients
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Publication Date
Fri Dec 01 2023
Journal Name
Baghdad Science Journal
Numerical Investigation of Physical Parameters in Cardiac Vessels as a New Medical Support Science for Complex Blood Flow Characteristics
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This study proposes a mathematical approach and numerical experiment for a simple solution of cardiac blood flow to the heart's blood vessels. A mathematical model of human blood flow through arterial branches was studied and calculated using the Navier-Stokes partial differential equation with finite element analysis (FEA) approach. Furthermore, FEA is applied to the steady flow of two-dimensional viscous liquids through different geometries. The validity of the computational method is determined by comparing numerical experiments with the results of the analysis of different functions. Numerical analysis showed that the highest blood flow velocity of 1.22 cm/s occurred in the center of the vessel which tends to be laminar and is influe

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