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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 Oct 01 2018
Journal Name
Iraqi Journal Of Physics
The study of thermal description for non-thermal plasma needle system
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Cold plasma is a relatively low temperature gas, so this feature enables us to use cold plasma to treat thermally sensitive materials including polymers and biologic tissues. In this research, the non-thermal plasma system is designed with diameter (3 mm, 10 mm) Argon at atmospheric pressure as well as to be suitable for use in medical and biotechnological applications.
The thermal description of this system was studied and we observed the effect of the diameter of the plasma needle on the plasma, when the plasma needle slot is increased the plasma temperature decrease, as well as the effect of the voltages applied to the temperature of the plasma, where the temperature increasing with increasing the applied voltage . Results showed t

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Publication Date
Wed Apr 05 2023
Journal Name
Journal Of Engineering
Study of the Friction Stir Welding For A516 Low Carbon Steel
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The main objective of present work is to describe the feasibility of friction stir welding (FSW) for
joining of low carbon steel with dimensions (3 mm X 80 mm X 150 mm). A matrix (3×3) of welding
parameters (welding speed and tool rotational speed) was used to see influence of each parameter on
properties of welded joint .Series of (FSW) experiments were conducted using CNC milling machine
utilizing the wide range of rotational speed and transverse speed of the machine. Effect of welding
parameters on mechanical properties of weld joints were investigated using different mechanical tests
including (tensile and microhardness tests ). Micro structural change during (FSW) process was
studied and different welding zones

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Publication Date
Sun Sep 30 2001
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Study the Characteristic Performance of Trickling Filter for Pharmaceutical Waste Treatment
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Publication Date
Sun Jul 01 2001
Journal Name
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A study of Immune Response in Golden Hamsters to Vaccinate against Leishmaniasis with Killed Promastigotes of Leishmania tropica
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Publication Date
Sun Dec 05 2010
Journal Name
Baghdad Science Journal
A study of some Biological Aspects of Procellio scaber(Isopoda : porcellionidae) Latrellile 1804In Al-jadriyia region /Baghdad-Iraq
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A study of some biological aspects of the crustacean Isopod procellio scaber was carried out for the period April 2003 to march 2004 . The study consisted reproductive and morphological characteristies such as size , weight and length of the body . The result showed that the highest population density of P. scaber was 1120 individual/m2 in September 2003 and less density 403 ind/m2 in February 2004. The density was generally high in Spring and Autumn, low in Summer and Winter months.An increase of the sexual ratio appear in the females number compared to males number (p < 0.05) during most of year. Present study showed non significant increase in the length and dry weight for females compared to males in most of year months. There wer

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Publication Date
Sun Jul 01 2018
Journal Name
Comprehensive Psychiatry
Complexity analysis of spontaneous brain activity in mood disorders: A magnetoencephalography study of bipolar disorder and major depression
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Publication Date
Fri Jun 17 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Clinicopathological analysis of 80 cases of oral lobular and non lobular capillary hemangioma (pyogenic granuloma): A Retrospective study
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Background: Oral pyogenic granuloma (PG) is a clinicopathological entity that could develop due to the reaction to a variety of stimuli, such as low-grade local irritation, traumatic damage, and hormonal stimulation. There are two histopathological types of pyogenic granuloma; lobular type -capillary hemangioma (LCH) and non-lobular type; with PG,LCH has highly vascular, diffuse capillary growth while non- lobular variant mimicking granulation tissue with heavily inflammated stroma. The study aims were to review the clinical  and histopathological spectrum of an oral pyogenic granuloma from different intraoral sites in order to avoid diagnostic pitfalls associated with similar morphological lesions and to determine

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Publication Date
Wed Apr 01 2015
Journal Name
Al–bahith Al–a'alami
Methods of US propaganda in Iraq- A Study of Coalition Provisional Authority and US Army Data after 2003
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with an organized propaganda campaign. This military campaign was helped to formulate its speech by many institutions, research centers, and knowledge and intelligence circles in order to mobilize public opinion gain supporters and face the opponents by different means depending on a variety of styles to achieve its required effects. 
          After the US occupation of Iraq, US media fighters sought to influence the Iraqi public opinion and making them convinced them of the important presence of US military forces in Iraq which necessitated finding its justification through the use of persuasive techniques in its intensive propaganda campaigns. 
  This research discusses the most important

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
A study of some physical, chemical and biological properties of Slabiaat River waters in Al-Muthanna province, Iraq
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Present study was conducted in order to assess Slabiaat water quality by measuring some physical and chemical factors of river water, the study included a choice of three stations along of Slabiaat River in Samawa city, water samples collected a monthly during the period from September 2013 August 2014. The study involved measuring the Air & water temperatures, pH, Electrical conductivity, Total dissolved solids, Dissolved oxygen, Total hardness, calcium hardness, magnesium, turbidity, and some types of bacteria in River water. The study results showed that the values of air & water temperatures have ranged between (20.1-36.6)?C , (10-21.8) in Slabiaat River, respectively . pH values ranged between (6.6-8.7). Electrical conductivity in

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Publication Date
Fri Nov 09 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Assessment of students' knowledge about environmental health in College of Health and Medical Technology: A Cross-Sectional study
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Objective: the aim of this study is to determine the level of students' knowledge about the environmental health.
Methodology: The cross-sectional study was conducted at the College of Health and Medical Technology in Baghdad
city during the period from 1st march till 1st of July 2012. Data was collected by self-recording of a previously designed
questionnaire to obtain socio-demographic information such as (age, gender, department, year of grade).
Results: The highest rate of students were in the 2nd year followed by the 3rd year, highest rate of students had low
level of knowledge followed by intermediate level of knowledge, while lowest rate of students on had high level of
knowledge .Females had higher level of know

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