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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 Jun 07 2009
Journal Name
Baghdad Science Journal
Investigation of the Optical Properties of the Achromatic Quadrupole Lens by Using the Rectangular Potential Distribution Model
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An optimization calculation is made to find the optimum properties of combined quadrupole lens which consists of electrostatic and magnetic lens. Both chromatic and spherical aberration coefficients are reduced to minimum values and the achromatic aberration is found for many cases. These calculations are achieved with the aid of transfer matrices method and using rectangular model of field distribution, where the path of charged-particles beam traversing the field has been determined by solving the trajectory equation of motion and then the optical properties for lens have been computed with the aid of the beam trajectory along the lens axis. The computations have been concentrated on determining the chromatic and spher

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Publication Date
Mon Sep 30 2024
Journal Name
Modern Sport
The Effect of Skill Exercises According to the Concentration Technique of Lateral Thinking on Motor Accuracy and Learning the Diving Stop Attack for Students in the Epee Weapon
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لمعرفة مدى تأثير تمرينات مهارية وفق تقنية تركيز للتفكير الجاني على الدقة الحركة وتعلم هجمة الإيقاف  بالغطس للطلاب في سلاح الشيش استخدمت الباحثتان المنهج التجريبي على عينة من طلاب المرحلة الثالثة بكلية التربية البدنية وعلوم الرياضة –جامعة ديالى والتي بلغت (30) طالباً موزعين على مجموعتين التجريبية والضابطة وبعد إكمال اجراءات البحث وتطبيق الاختبارات القبلية وتنفيذ التمرينات والاختبار البعدي ومعالجة الب

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Publication Date
Tue Jan 01 2019
Journal Name
African Journal Of Hospitality, Tourism And Leisure
Employing marketing information systems for the success of small and medium enterprises: A field study of some Tourism and Travel companies in Baghdad
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Publication Date
Thu Mar 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
(The Segmentation of Industrial Market and its Effect in Targeting Market : An descriptive analytical study for a sample of industrial companies in Iraq)
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 This study deals with segmenting the industrial market as an independent variable and targeting the industrial market as a dependent variable. Since the industrial sector represents one of the most important fundamental pillars to build the economies of countries and their development , the Iraqi industrial sector was chosen as a population for the study . Based on measuring the study variables , identifying them and testing the correlation and effect on each other , the study reached a group of findings:

1- Increasing the level of availability of study variables inside the companies “The study sample”.

2- There is a correlation between the independent v

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Publication Date
Wed Dec 29 2021
Journal Name
Al-khwarizmi Engineering Journal
Comparison of Prediction Programs for Short Wave Circuit Link from Iraq to Test points on Both Earth Hemispheres during Solar Minimum
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This paper compare  the accurecy of HF propagation  prediction programs for  HF circuits links between Iraq and  different points world wide  during August 2018 when  solar cycle 24 (start 2009 end 2020) is at minimun activity and also find out the best communication mode  used. The prediction   programs like Voice of America Coverage Analysis Program (VOACAP) and ITU Recommendation RS 533 (REC533 )  had been used to generat HF circuit link  parameters like Maximum Usable Frequency ( MUF) and Frequency of Transsmision (FOT) .Depending  on the predicted parameters (data)  , real radio contacts had been done using a radio transceiver from Icom  model IC 7100 with 100W RF

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Publication Date
Wed Sep 07 2016
Journal Name
Journal Of The Faculty Of Medicine
Non discogenic lumbar radiculopathy ((A study of 104 cases))
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AW Ali T, Journal of the Faculty of Medicine, 2016 - Cited by 1

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Publication Date
Fri Nov 03 2023
Journal Name
Lecture Notes In Electrical Engineering
A Survey Study and Comparison of Drones Communication Systems
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Publication Date
Thu Jun 01 2023
Journal Name
Journal Of Composite Materials
Fabrication and characterization of bioactive composite: A pilot study
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The increasing requirement and use of dental implant treatments has rendered dental implantology indispensable in dentistry. The aim of this study is to determine the optimum concentration of calcium silicate to be incorporated into a polyetherketoneketone (PEKK) matrix used as an implant material to enhance the bioactivity and mechanical properties of the composite compared with unmodified PEKK. In this study, different weight percentage (wt%) of micro-calcium silicate (m-CS) is incorporated into PEKK with ethanol as a binder. Subsequently, the mixture is dried in a forced convection oven at 120°C and poured into customized molds to fabricate a bioactive composite via compression molding (310°C, 15 MPa, and 20 min holding time

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Publication Date
Sat Apr 24 2021
Journal Name
Turkish Journal Of Computer And Mathematics Education (turcomat)
A Linguistic Study of Epitaphs in Selected English Texts
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This research aims at analysing epitaphs written by Thomas Moore for the memory of Rupert Southey, the epitaph is analysed linguistically and stylistically on four levels graphology, phonology, morphology, and lexico-syntax level to explore the elements that the writer uses the most at each level. Bearing in mind Nowottny approach (1962) (to text analysis) who believes that the linguistic analysis of a literary text is not just a marginal but a necessity” (Bakuuro etal., 2018:34). The researcher has selected and analysed a written epitaph of famous individual associated with English, literature. The study involves both literary and linguistic analysis, with much more concentration through the analysis on the aspect of linguistics. In fact

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Publication Date
Tue Mar 01 2022
Journal Name
Bulletin Of The Australian Mathematical Society
A DYNAMICAL STUDY OF SALINE PLUMES IN DESALINATION OUTFALLS
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