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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
Tue Aug 07 2018
Journal Name
Oral And Maxillofacial Surgery
Mandibular war injuries caused by bullets and shell fragments: a comparative study
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Publication Date
Sun Jun 07 2015
Journal Name
Baghdad Science Journal
A comparative study to determine the nature of the eye lens protein in the two types of birds Iraqi
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The study showed significant differences between the average weight lens and the average amount protein in the lens between that Kestrel Falco tinnunculus L. and the Collared Dove Streptopelia decaocto F. , also the study electrical migration of lens proteins having one bundle of crystalline –? in Kestrel compared with three bundles in Collared Dove, two bundles of crystalline – ? in both , and crystalline – ? appeared as one bundle in both birds.

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Publication Date
Mon Nov 19 2018
Journal Name
Al–bahith Al–a'alami
Analytical Study of Cartoon picture AL-Mada Newspaper is a model
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The researcher studies and explains the content of some pictures that are published in al-Mada newspaper. The research is important as it deals with a topic that has a relation with visual culture and its role to transfer the press letter to the audience. The researcher finds that cartoonist exposed the security services through important people who have a major role in state policy and reveals the level of corruption and the weak treatments for this phenomenon and its reflection on the whole society and individuals. In addition to that, cartoonists try to encourage the public for going on the peaceful demonstrations since it is a good tool to make pressure on the government to punish the corrupts.

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Publication Date
Mon Dec 31 2018
Journal Name
Ibn Al-haitham Jour. For Pure & Appl. Sci
Comparative Study of Thymidine Kinase -1 and Total Antioxidant Capacity in Iraqi Children with Platelet Count Disorder
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This study aimed to find relationship between thymidine kinase-1 (TK-1) as tumor marker and total antioxidant capacity (TAC) in Iraqi children patients with thrombocytopenia and with thrombocytosis. The present study conducted 60 children patients (30 patients with idiopathic thrombocytopenia purpura (ITP) and 30 patients with thrombocytosis caused by leukemia) attending the Children Fever Hospital in the Medical City / Baghdad, and 30 healthy children as a control group. All study groups were with range ages (1-15) years, and they were diagnosed by assay of platelet count, Prothrombin Time (PT), and partial Thromboplastin Time (PTT). The results shown elevation in plasma TK-1 and TAC values in children patients with thrombocytopenia and w

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Publication Date
Fri Aug 12 2016
Journal Name
Iraqi Dental Journal
Pacifier Sucking Habit and its Relation to Oral Health of Children Aged 1-5 Years (comparative study)
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Publication Date
Sat Dec 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Selecting Optimum Dimensions for a Three-Phase Horizontal Smart Separator for Khor Mor Gas-Condensate Processing Plant
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      The Khor Mor gas-condensate processing plant in Iraq is currently facing operational challenges due to foaming issues in the sweetening tower caused by high-soluble hydrocarbon liquids entering the tower. The root cause of the problem could be liquid carry-over as the separation vessels within the plant fail to remove liquid droplets from the gas phase. This study employs Aspen HYSYS v.11 software to investigate the performance of the industrial three-phase horizontal separator, Bravo #2, located upstream of the Khor Mor sweetening tower, under both current and future operational conditions. The simulation results, regarding the size distribution of liquid droplets in the gas product and the efficiency gas/liquid separation, r

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Publication Date
Sat Oct 03 2020
Journal Name
International Journal Of Pharmaceutical Research
Serum Afamin As A Novel Biomarker for NonAlcoholic Fatty Liver Disease as A Complication of Hypothyroidism in Iraqi Patients.
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Afamin, which is a human plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome. Afamin concentration have been proposed to have a significant role as a predictor of metabolic disorders. Since NAFLD is associated with metabolic risk factors, e.g., dyslipidemia, insulin resistance and visceral obesity, it is considered as the hepatic manifestation of the metabolic syndrome. The objective of this study is to determine Afamin levels in hypothyroid patients with and without fatty liver disease and compare the results with controls. Also to study the relationship of Afamin level with the Anthropometric and Clinical Features (Age, Gender, BMI and Duration of Hypothyroidism) , Serum

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Publication Date
Mon Feb 19 2018
Journal Name
Al-academy
The Mechanisms of build up the dramatic construction in the films of the world of nature - National Geographic's films as a model-
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The subject of  research entitled "The Mechanisms of build up the dramatic construction in the films of the world of nature - National Geographic's films as a model" emerges from the importance of the subject of the dramatic construction and its departure from its classic style due to the evolution of the visual  presentation and its instruments and the specificity and emergence of a form of television production represented by the films of the world of nature which began to occupy an important space in the map of television and television channels specialized in this subject, which drove the researcher to study the mechanisms of producing the dramatic construction in this kind of film s. This research came in three  chapt

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Publication Date
Sun Sep 02 2012
Journal Name
Baghdad Science Journal
Preparation of PVC composite using reinforced Iraqi Bentoniet clay as a filler & study their mechanical and thermal properties
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In this study , Iraqi Bentonite clay was used as a filler for polyvinyl chloride polymer. Bentonite clay was prepared as a powder for some certain particle size ,followed by calcinations process at (300,700,900) OC ,then milled and sieved. The selected sizes were D ~75 µm and D ~150. After that polyvinyl Al-Cohool solution prepared and used as a coated layer covered the Bentonite powder before applied as a filler ,followed by drying , milling and sieving for limited recommend sizes. polyvinyl chloride solutions were prepared and adding of modified Bentonite power at certain quantities were followed .Sheet of these variables on the mechanical and thermal properties of the prepared reinforced particular polyvinyl chloride composite

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Publication Date
Thu Nov 01 2012
Journal Name
Journal Of The Faculty Of Medicine Baghdad
A Comparative Study of the Effects of Age and Smoking on Nail Growth Rate in Healthy Individuals
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GA Al Omran, AA Noaimi, Z Al Madfai, H Al Hamamy, Journal of the Faculty of Medicine Baghdad, 2012

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