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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
Wed Jan 01 2025
Journal Name
Science Progress
Impact of COVID-19 on the prevalence of oral and maxillofacial disorders: A retrospective cohort study
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Publication Date
Sun Mar 30 2003
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Mathematical Model for Multicomponent Distillation Column
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Publication Date
Wed Feb 01 2023
Journal Name
Journal Of Engineering
Applying the WaterGEMS Software to Conduct a Comparison of the Darcy-Weisbach and Hazen-Williams Equations for Calculating the Frictional Head Loss in a Selected Pipe Network
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Darcy-Weisbach (D-W) is a typical resistance equation in pressured flow; however, some academics and engineers prefer Hazen-Williams (H-W) for assessing water distribution networks. The main difference is that the (D-W) friction factor changes with the Reynolds number, while the (H-W) coefficient is a constant value for a certain material. This study uses WaterGEMS CONNECT Edition update 1 to find an empirical relation between the (H-W) and (H-W) equations for two 400 mm and 500 mm pipe systems. The hydraulic model was done, and two scenarios were applied by changing the (H-W) coefficient to show the difference in results of head loss. The results showed a strong relationship between both equations with correlation coefficients of 0.999,

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Publication Date
Sun Mar 03 2013
Journal Name
Baghdad Science Journal
Molecular Diagnosis of Brucella species in Baghdad
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Brucellosis is possess a significant public health problem in Baghdad. In this study, we investigated the potential role of the PCR assay in detection of Brucella species, from patients suspect to have brucellosis, using blood samples in both human and animal. To establish a PCR technique for diagnosis of active brucellosis in our samples, DNA extraction was carried out using a commercial kit, and a laboratory extraction procedure. PCR amplification was done using 1 set of primers: B4/B5 for Brucella species. Extraction of Brucella DNA using the commercial kit was successful. The laboratory extraction was successful and more economic. A total of 178 peripheral blood

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Publication Date
Tue Jan 01 2013
Journal Name
Advances In Physics Theories And Applications
Adsorption Study of Symmetrical Schiff Base Ligand 4,4’-[hydrazine-1,2-diylidenebis(methan-1-yl-1-ylidene) bis (2-methoxyphenol)] on Granulated Initiated Calcined Iraqi Montmorillonite via Columnar Method.
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The adsorption ability of Iraqi initiated calcined granulated montmorillonite to adsorb Symmetrical Schiff Base Ligand 4,4’-[hydrazine-1, 2-diylidenebis (methan-1-yl-1-ylidene)) bis (2-methoxyphenol)] derived from condensation reaction of hydrazine hydrate and 4-hydroxy-3-methoxybenzaldehyde, from aqueous solutions has been investigated through columnar method.The ligand (H2L) adsorption found to be dependent on adsorbent dosage, initial concentration and contact time.All columnar experiments were carried out at three different pH values (5.5, 7and 8) using buffer solutions at flow rate of (3 drops/ min.),at room temperature (25±2)°C. The experimental isotherm data were analyzed using Langmuir, Freundlich and Temkin equations. The monol

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Publication Date
Mon May 27 2019
Journal Name
Al-academy
The Aesthetic Approaches to Dialectical Development in the Functions of Contemporary Theater Director ) Macbeth Play Directed by Salah al-Qasab a Model (: ثابت رسول جواد
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The current research studies the aesthetic framework for the dialectical development of the functions of the contemporary theater director in an aesthetic approach to the mechanisms of functional overlap between the dramaturgy and direction functions, and scenography and direction, the detection of the controversial structure of that overlap, and what can be summed up in the following question: (what are the aesthetic approaches of the dialectical development in the function of the contemporary theatre director?). The research is determined by a pivotal aim which is (knowing the aesthetic nature of the dialectical development in

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Publication Date
Tue Sep 15 2020
Journal Name
Al-academy
Forbidden Montage and the transition Technique in one-snapshot Movies 1917 Film- A model: محمد عبد الجبار كاظم-عذراء محمد حسن
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  Starting from the term (forbidden montage) initiated by the French critic (Andre Bazin) as a method of processing the movies that depend on (mise en scene) achieved by the action of the camera and its ability to photograph and employ the depth of the field, in addition to the possibility of free movement without interruption in the filming environment in order to avoid montage as much as possible (the montage that distorts focus and distracts attention and moves away from realism, which is the most important theoretical pillar of Bazin in photography). The pursuit was behind a cinema that depicts its topics in one integrated snapshot with all its details thus approximating reality without any interference of montage. Our study sta

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Publication Date
Thu Oct 01 2020
Journal Name
Wireless Communications And Mobile Computing
Developing a real time navigation for the mobile robots at unknown environments
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<p><span>This research deals with the feasibility of a mobile robot to navigate and discover its location at unknown environments, and then constructing maps of these navigated environments for future usage. In this work, we proposed a modified Extended Kalman Filter- Simultaneous Localization and Mapping (EKF-SLAM) technique which was implemented for different unknown environments containing a different number of landmarks. Then, the detectable landmarks will play an important role in controlling the overall navigation process and EKF-SLAM technique’s performance. MATLAB simulation results of the EKF-SLAM technique come with better performance as compared with an odometry approach performance in terms of measuring the

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Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Al-nahrain University Science
A Lexical and Syntax Checker Tool for the Hyper Text Markup Language
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Publication Date
Tue Jun 02 2009
Journal Name
Albahith Alalami
A proposed scientific strategy for public relations activity at the Integrity Authority.
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This study deals with knowing the public relations activities of the Integrity Commission for the year 2007, knowing the contents of these activities, knowing the contents of the advertisements that it published, whether the contents of the advertisements were convincing, and whether press photographs were used in these advertisements, as well as whether symbols and slogans were used. What language and words were used to address the recipient? 1- What feelings do the contents of advertisements arouse? 2- Research objectives: This research aims to answer the following questions: What are the public relations activities carried out by the Integrity Commission? B: Are the contents of the advertisements published by the Authority convincing to

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