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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 Jan 01 2023
Journal Name
International Journal Of Drug Delivery Technology
Phytochemical Investigation and Pharmacological Activity of Solidago canadensis L. against H1N1 Virus, involving the Separation and Identification of Three New Compounds
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Publication Date
Fri Aug 26 2022
Journal Name
Journal Of Contemporary Medical Sciences
Measurement of the serum level of Leucine-rich alpha-2-glycoprotein-1 in hospitalized Iraqi COVID-19 Patients
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Objective: The study aimed to assess Leucine-rich alpha-2-glycoprotein-1 biomarker serum level in hospitalized COVID-19 patients. Methods: The case control study from multi-centers in Baghdad included 45 adult patients (19 females and 26 males) with COVID-19, diagnosed with a positive real-time reverse transcription polymerase chain reaction and excluded negative RT-PCR for COVID-19 and comorbidity conditions. Second group, was 43 control (20 females and 23 males). Results: This study found a decrease Leucine-rich alpha-2-glycoprotein-1 biomarker serum level in these patients and a significant difference in D. dimer, neutrophil count, lymphocyte count, and the neutrophil-lymphocyte ratio between the patients and controls at a P valu

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Publication Date
Wed Jan 01 2020
Journal Name
International Conference Of Numerical Analysis And Applied Mathematics Icnaam 2019
Investigate of TiO2 and SnO2 as electron transport layer for perovskite solar cells
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Publication Date
Wed Jul 01 2015
Journal Name
J Fac Med Baghdad
AH jump as predictor for successful Ablation of atrioventricular nodal reentrant tachycardia (AVNRT)
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Background: Atrioventricular nodal reentrant tachycardia (AVNRT) is the commonest regular supraventricular tachyarrhythmia. Ablation in the area of slow pathway (SP) has been successfully implemented in every day clinical electrophysiological practice for more than 20 years. Although the procedure is generally regarded as effective and safe, data on long-term effects and predictors of success or failure are incomplete.

Publication Date
Sun Mar 04 2018
Journal Name
Baghdad Science Journal
Using Texture Analysis Image Processing Technique to Study the Effect of Microwave Plasma on the Living Tissue
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The present study is a hybrid method of studying the effect of plasma on the living tissue by using the image processing technique. This research explains the effect of microwave plasma on the DNA cell using the comet score application, texture analysis image processing and the effect of microwave plasma on the liver using texture analysis image processing. The study was applied on the mice cells. The exposure to the plasma is done by dividing the mice for four groups, each group includes four mice (control group, 20, 50, 90 second exposure to microwave plasma). The exposure to microwave plasma was done with voltage 175v and gas flow on 2 with room temperature; the statistical features are obtained from the comet score images and the textur

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Publication Date
Mon Nov 06 2023
Journal Name
Eneurologicalsci
Dandy-Walker syndrome associated with a giant occipital meningocele: A case report and a literature review
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HTH Ahmed Dheyaa Al-Obaidi,", Ali Tarik Abdulwahid', Mustafa Najah Al-Obaidi", Abeer Mundher Ali', eNeurologicalSci, 2023

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Publication Date
Wed Jun 29 2022
Journal Name
Journal Of The College Of Education For Women
The Reality of Teachers’ Use of Modern Technologies in Teaching Arabic as a Second Language in Terms of Objectives and Selection Foundations at the Institute of Arabic Language in Umm Al-qura University Mamoun Eltigani Hassan Eldali
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This study aims to know the degree of importance and the availability of the enhancing specifications of the educational process, and the way its objectives are achieved. Such a step involves using educational techniques, laying the selection foundations, knowing the methods of their employment and tracking the obstacles that limit this employment in teaching Arabic to non-native speakers. To achieve these objectives, the study followed a descriptive approach, and collected the necessary data through an integrated questionnaire prepared for the purpose of describing the phenomenon or topic. This approach was adopted, as it is characterized by being comprehensive, focuses on collecting data related and necessary to the topic under study.

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Publication Date
Sun Oct 01 2017
Journal Name
مجلة القادسية للعلوم الرياضية
The impact of leverage in two different environments on the development of weapons and arms explosion strength on some physiological indicators and the accuracy of the performance of the service and crushing volleyball skills
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ھدف البحث الـــــى : ١ -إعداد تدریبات القوة الارتدادیة في وسطین متباینین على بعض المؤشرات الفسیولوجیة لتطویر القوة الانفجاریة ودقة مھارتي الأرسال والضرب الساحق بالكرة الطائرة . ٢ -التعرف على تأثیر تدریبات القوة الارتدادیة في وسطین متباینین على بعض المؤشرات الفسیولوجیة لتطویر القوة الانفجاریة.. ٣ -التعرف على تأثیر تدریبات القوة الارتدادیة في وسطین متباینین على دقة مھارتي الأرسال والضرب الساحق بالكرة الطائرة

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Publication Date
Sat Jun 30 2012
Journal Name
Al-kindy College Medical Journal
VCAM-1 Expression in Endometerium with Human Cytomegalovirus Infection
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Background: To elucidate the possible role of human cytomegalovirus in pregnancy loss through induction of certain pro-inflammatory adhesion molecules.
Methods: Paraffin embedded sections of curate samples were obtained from 34 women had spontaneous abortion, and 5 women had elective termination of pregnancy (as control), and then subjected for immunohistochemistry analysis to detect human cytomegalovirus (HCMV) early protein and VCAM-1 molecule.
Results: Nine out of 34 women with spontaneous abortion were positive for HCMV early protein, with a
significantly higher expression of VCAM-1 in HCMV positive cases as compared with HCMV negative and the control groups (p = 0.05, 0.001 respectively).
Conclusion: HCMV infection may p

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
The Image of the Soldier in Brendan Behan's The Hostage And Charles Fuller's A Soldiers Play: The Image of the Soldier in Brendan Behan's The Hostage And Charles Fuller's A Soldiers Play
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Abstract
The image of the soldier, as a hero who sacrifices everything to defend his
country and values, is no longer depicted in modern drama. With two World Wars
and many regional wars and civil wars, the soldier becomes a victim, not a hero.
Authors present the character of the soldier as a man who suffers a lot as he is
victimized by his own government and its politics that forces him to be in such a
position. Dramatists express their views about race, oppression and war through
their characters, such as the character of the soldier, as in the two selected plays for
this research: The Hostage by Brendan Behan and A Soldier's Play by Charles
Fuller.
The Hostage depicts, through its events, the Irish oppre

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