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bijps-1604
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 Mar 07 2010
Journal Name
Baghdad Science Journal
The Direct Gene Injection Using of Egg Yolk Emulsion as Carrier and its Comparison with Liposomes.
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The efficiency of egg yolk emulsion in coating DNA and its delivery across cellular membranes was evaluated in comparison with liposomes DOPE . The murine leukemia viral oncogene v-abl , cloned on pBR322 was used as a DNA substrate for direct injection into mice tissue . the DNA complexes were prepared by mixing the DNA with egg yolk emulsion and liposome . Each was directly injected into mice peritoneal cavity with proper control. The gene delivery was examined phenotypically by blood analysis and cytogenetic analysis . Chromosomal changes were detected in the bone marrow as from the fourth day post inoculation through the eleventh day when chromosomal ring s could be seen . this was accompanied by decrease in the WBC count ,

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Publication Date
Tue Aug 02 2016
Journal Name
European Academic Research
‘Resymbolization’ of a Text; a Relatively Different Perspective of Graham Greene’s The Quiet American
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The Quiet American could be considered as one of Graham Greene’s most distinguished books; it is an epochal novel written during the phase of the cold war between the United States and the Soviet Union. The novel deals with the interference of the United States in Vietnam ten years before Vietnam’s war. The role the Americans played in arousing an inner political crisis in the country previous to her military invention. The book reflects that this action was not out of American government concern about Vietnamese people themselves but merely a political foreign affair. They wanted to stop communism from spreading widely and reducing its role in the East. This paper attempts to analyse the novel concentrating on the message Greene intend

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
Imams al-Imam al-Bazazi (AH827) in his book al-Fatawi al-Bazazi issues purity is a model
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The study included three topics, the definition of the personality of Imam al-Bazazi, his scientific biography, his elders, his writings, his students and his death, selected issues of his weightiness related to purity, and the Imam al-Bazazi is Muhammad ibn Muhammad ibnShihabibn Yusuf, known in al-Kardari al-Hanafi al-Balzazi. The other doctrines, the author relied in his book on the sources of the previous scholars of the Hanafis, and make them the basis in his book, the author did not adopt the definitions of language and terminology, and rarely mention the evidence Shariah adopted by scientists in their opinions, and limited to mention only opinions, In front of the first issue spotlessly water user, and the second issue that sleep l

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Comparison of HF and HCl Chemical Laser Parameters by using Mathematical Model
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A simplified theoretical comparison of the hydrogen chloride (HCl) and hydrogen fluoride (HF) chemical lasers is presented by using computer program. The program is able to predict quantitative variations of the laser characteristics as a function of rotational and vibrational quantum number. Lasing is assumed to occur in a Fabry-Perot cavity on vibration-rotation transitions between two vibrational levels of hypothetical diatomic molecule. This study include a comprehensive parametric analysis that indicates that the large rotational constant of HF laser in comparison with HCl laser makes it relatively easy to satisfy the partial inversion criterion. The results of this computer program proved their credibility when compared with th

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Publication Date
Wed Sep 11 2019
Journal Name
Aip Conference Proceedings
Estimation of shock wave position in plasma plume using Sedov-Taylor model
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In this work, radius of shock wave of plasma plume (R) and speed of plasma (U) have been calculated theoretically using Matlab program.

Publication Date
Wed Feb 10 2016
Journal Name
ألمؤتمر الدولي العلمي الخامس للاحصائيين العرب/ القاهرة
Proposition of Modified Genetic Algorithm to Estimate Additive Model by using Simulation
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Often phenomena suffer from disturbances in their data as well as the difficulty of formulation, especially with a lack of clarity in the response, or the large number of essential differences plaguing the experimental units that have been taking this data from them. Thus emerged the need to include an estimation method implicit rating of these experimental units using the method of discrimination or create blocks for each item of these experimental units in the hope of controlling their responses and make it more homogeneous. Because of the development in the field of computers and taking the principle of the integration of sciences it has been found that modern algorithms used in the field of Computer Science genetic algorithm or ant colo

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Publication Date
Thu Jun 20 2024
Journal Name
Bulletin Of The Iraq Natural History Museum
MOLECULAR STUDY OF SOME SPECIES OF CENTIPEDES IN IRAQ WITH NEW RECORD OF LITHOBIUS CRASSIPES L. KOCH, 1862 (CHILOPODA, LITHOBIOMORPHA, LITHOBIIDAE)
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The first molecular research on Iraqi centipede fauna is presented in this article. Between October 2022 and May 2023, during various climatic circumstances, centipedes were collected from several locations in four provinces of Iraq. Three families, represented by four genera, underwent molecular identification, and five species were found. From the order Scolopendromorpha family Scolopendridae, two species were recorded, Scolopendra morsitans Linnaeus, 1758, and S. cingulata Latreille, 1829, Cormocephalus sp.; while from the order Lithobiomorpha, family Lithobiidae, one species was recorded for first time in Iraq; Lithobius crassipes L. Koch, 1862 from the order Geophilomorpha family Himantariidae, one species Bothriogaster Signata

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Qualification Of Human Resources To Apply Electronic Management A case study In The Ministry Of Science And Technology
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     This research aims to shed light on the reality of the process of rehabilitation of human resources for the implementation of electronic management practice in the ministry, and availability requirements of the application of electronic management and diagnosis of the most important stages and steps that can be followed in the process of transition towards electronic management to keep abreast of developments in the field of information technology, has been the application of this research in the Ministry of science and technology on a group of heads of departments and directors of the people in the departments of the Ministry through the use of case study method, which includes cohabitation field intervi

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Publication Date
Fri Mar 31 2017
Journal Name
Al-khwarizmi Engineering Journal
Experimental Study to the Effect of Natural Particles Added to Unsaturated Polyester Resin of a Polymer Matrix Composite
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Experimental investigations had been done in this study to demonstrate the effect of natural particles used as a reinforcement material to unsaturated polyester resin. The tensile test and water absorption were investigated according to (ASTM D638) and (ASTM D570), respectively. The influence of sunflower husk and pomegranate husk particles, used as a reinforcement material, on the tensile strength, Young's modulus and water absorption with different weight fraction (3%, 7% and 10%) and particle grain size (50µm, 100 µm and 150 µm), has been investigated. The water absorption of polymer composites was studied by measuring the specimen weight before and after immersion in water for one hundred days. In the experiments of tensile test,

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Publication Date
Mon Sep 30 2019
Journal Name
College Of Islamic Sciences
Detailed interpretation of Sheikh Abdullah Knon A look at the curriculum and method of innovation Critical inductive study
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The problem lies in the main research Where the site of this interpretation of the books of interpretation and what is new and how?
The objectives of this research Vjat to give a quick overview of Sheikh Kenon and the qualifications that made him interpreter, as the goal of the research to reveal the method of Sheikh Kenon highlighting what he has and what is new and show.
The researcher used the inductive method to read the whole book and the comparative approach to compare it with others. He also used the critical method to distinguish between the positions of strength and weakness in the book. The most important results are as follows: :
1 - Sheikh Abdullah Kenon language writer familiar with many sciences, such as jurisprude

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