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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 Mar 01 2021
Journal Name
Journal Of Physics: Conference Series
Structural, surface morphology and optical properties of annealing treated Copper Phthalocyanine doped Fullerene (CuPc: C<sub>60</sub>) thin films
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Abstract<p>The doping process with materials related to carbon has become a newly emerged approach for achieving an improvement in different physical properties for the obtained doped films. Thin films of CuPc: C<sub>60</sub> with doping ratio of (100:1) were spin-coated onto pre-cleaned glass substrates at room temperature. The prepared films were annealed at different temperatures of (373, 423 and 473) K. The structural studies, using a specific diffractometry of annealed and as deposited samples showed a polymorphism structure and dominated by CuPc with preferential orientation of the plane (100) of (2θ = 7) except at temperature of 423K which indicated a small peak around (2θ = 3</p> ... Show More
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Publication Date
Fri Dec 01 2023
Journal Name
Baghdad Science Journal
Heat Production Rate and Radiation Hazard Indices from Radioactive Elements in Different Types of Natural Water in Nineveh Governorate, Iraq.
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The current study sheds light on the measurement and estimation of the radioactivity of radionuclides (238U, 226Ra, 232Th, and 40k) in natural waters of different regions of Nineveh Governorate in Iraq.15 samples were collected from different sources of natural waters, where gamma-ray spectroscopy was used using NaI)TI) sodium iodide detector to determine the concentration of radioactivity in the samples. According to the results, the radioactivity concentration in the tested water sample were ​​ranged from 0.36 ± 0.04-1.57 ± 0.09with an average value of 0.69 ± 0.06 Bq/l for 238U, and 2.9 ± 0.02-0.88 ± 0.03 with an average value of 0.65 ± 0.03 Bq/l for 226Ra Bq/l

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Publication Date
Sun Dec 25 2016
Journal Name
University Of Baghdad / College Of Education For Pure Sciences / Ibn-al-‎haitham/ Chemistry Department
Synthesis and Spectroscopic Studies and ‎Biological Activity of New Ligands ‎Containing S,N,O Donor Atoms with their ‎Metal Complexes
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The 3-aminoacetophenone and 4-aminoantipyrine were used as ‎precursors to prepare new six ligands. The three new ligands (L1,L2 ‎and L3) were synthesis by reacting one mole of 3-aminoacetophenone ‎with one mole of (Acetyl chloride), (benzoyl chloride), (4-‎methoxybenzoyl chloride) and ammonium thiocyanat in acetone as a ‎solvent, they are:-‎ L1 (AAA) =[N-(3-acetylphenylcarbamothioyl)acetamide]‎ L2 (BAA) =[N-(3-acetylphenylcarbamothioyl)benzamide]‎ L3 (MAA) =[N-(3-acetylphenylcarbamothioyl)-4-methoxy benzamide]‎ Also three new derivatives of 4-aminoantipyrine were synthesis by ‎reacting one mole of 4-aminoantipyrine with one mole of (Acetyl ‎chloride), (benzoyl chloride), (4-methoxybenzoyl chloride) and ‎ammonium thio

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Publication Date
Sat Nov 10 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Impact of Socio-economic Status on Age at Menarche among Secondary School Students at AL-Dora Region in Baghdad Governorate
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Objective: To assess the Impact of Socio-economic status on age at menarche among secondary school students at
AL-Dora city in Baghdad, Iraq.
Methodology: This is a cross sectional study with multi-stage sampling was carried out during the period from the
3
th of December2013 to 12th of March 2014. The Sample comprised of 1760 girls, 1510 girls from urban area and
250 from rural area was included in the study. In first stage, selection of schools was done, and one class was
selected randomly from each level of Education, The data collection through a special questionnaire which Contain
the age of girl by year, class level, birth order, number of household, number of rooms, residency (urban/rural),
education level

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Publication Date
Thu Feb 16 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Cost-effectiveness Analysis of Reference Infliximab (Remicade) Compared to its Biosimilar (Remsima) in Iraqi Patients with Rheumatoid Arthritis (Conference Paper )#
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The study objective was to conduct Pharmacoeconomics study (cost-effective analysis) between infliximab reference (Remicade) and its biosimilar (Remsima) in patients with rheumatoid arthritis (RA) in Iraqi hospitals.

This is a retrospective multicenter pharmacoeconomic analysis conducted at two large teaching governmental hospitals in Baghdad, Iraq which provided infliximab to patients with RA. Data were collected from patient’s medical records and face-to-face interviews with the patients from December 2021 to April 2022.

The study included 57 patients with rheumatoid arthritis (RA).  The patients were categorized into two groups according to the type of infliximab they received over 30 weeks: 27 patients received

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Publication Date
Thu Oct 01 2020
Journal Name
Biochemical And Cellular Archives
CUT-OFF VALUES OF BLACKCURRANT, LONDON PLANE AND PINE BUDS ON VANCOMYCIN RESISTANT ENTEROCOCCI ISOLATED FROM MASTITIC MILK IN BAGHDAD
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Generation of new clones of multidrug resistant infectious foci of environmental, zoonotic and reverse zoonotic Enterococcus faecalis & faecium strains from cases of mastitis in cows privileged in Baghdad ecosystem reveal unsafe tricks. Medically important plants Blackcurrant, London Plane and Pine Buds are widely used for resolving these public health threats and hazards as powerful antimicrobial preparations. Totally sixty pooled milk samples were collected from apparently healthy (30 units) and infected (30 units) Cows from different regions of Abu-Ghraib during March until July (2019). Integrated units were checked by California mastitis test and a designed scheme was dependent for recovery of pathogenic Enterococci. Gram staining and c

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Publication Date
Mon Apr 03 2023
Journal Name
Journal Of Educational And Psychological Researches
Critical Thinking Skills of A’Sharqiah University Students According to California Critical Thinking Skills Test and Its Relationship to Some Variables
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Abstract

The research aims to measure the level of critical thinking skills among students of A’Sharqiah University in the Sultanate of Oman, as well as identify the level of their availability based on the variables: gender, academic level, school year, cumulative average, and general diploma / high school ratio. The researchers used the descriptive approach. To achieve the objectives of the study, they used The California Test for Critical Thinking Skills Picture (A) after evaluation (Farraj, 2006). It was applied to a sample of (487) students from A’sharqiah University. The results of the study found that the critical thinking skills of A’sharqiah University students are below the educationally acceptabl

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Publication Date
Thu Jun 30 2016
Journal Name
Al-kindy College Medical Journal
Antibacterial activity of Trigonella Foenum- groecum essential oil against skin infection with Staphylococcus aureus: In vitro and in vivo studies
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Background: Multi- drug resistant (MDR) Staphylococcus aureus infections have become a major public health concern in both hospital and community settings.Objective: to investigate the antibacterial activity of T. Foenum- groecum essential oil against skin infection with S. aureus and to study probable synergistic activity in combination with Clindamycin.Type of the study: Cross-sectional study.

Methods: Antibacterial activity of T. Foenum- groecum essential oil extract (1.2gm/100 µl) was investigated in multi- drug resistance (MDR) Staphylococcus aureus specimen isolated from patients with skin infection in Baghdad. T. Foenum- groecum use externally for cellulites and skin inflammation due to the presence of diosgenin .fast liq

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Publication Date
Sun Jun 09 2019
Journal Name
Al-kindy College Medical Journal
Early Detection of Left Ventricular Systolic Dysfunction in Asymptomatic Patients with Chronic Aortic Regurgitation by two Dimensional Speckle Tracking Echocardiography
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Background: Early detection of subclinical left ventricular (LV) systolic dysfunction is crucial and could influence patients' prognosis by aiding the clinician to candidate patients for better management.

Objective: To detect early LV systolic dysfunction in asymptomatic patient with chronic aortic regurgitation by two dimensional speckle tracking echocardiography.

 Methods:  Sixty one asymptomatic patients with chronic aortic regurgitation, with no ischemic heart diseases (by coronary angiography) or conductive heart diseases, no diabetes mellitus, no hypertension, and no other valvular heart diseases (group 1) and fifty age and sex-matched healthy subjects (

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Publication Date
Sun Dec 01 2019
Journal Name
Regenerative Therapy
In vitro periodontal ligament cell expansion by co-culture method and formation of multi-layered periodontal ligament-derived cell sheets
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Objective: Per-implantitis is one of the implant treatment complications. Dentists have failed to restore damaged periodontium by using conventional therapies. Tissue engineering (stem cells, scaffold and growth factors) aims to reconstruct natural tissues. The paper aimed to isolate both periodontal ligament stem cells (PDLSCs) and bone marrow mesenchymal stem cells (BMMSCs) and use them in a co-culture method to create three-layered cell sheets for reconstructing natural periodontal ligament (PDL) tissue. Materials and methods: BMMSCs were isolated from rabbit tibia and femur, and PDLSC culture was established from the lower right incisor. The cells were co-cultured to induce BMMSC differentiation into PDL cells. Cell morphology, stem cel

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