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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
Fri Jun 01 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The reality of corporate tax and its role in the tax Revenues in Iraq: An analytical study for the years 2005-2010
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This study showed the basic features of corporate tax in Iraq by showing what was in the Income Tax Law in force .The study aims of this to indicate the role of tax corprates in tax revenue and then the possibility of strengthening the revenue of this tax as an important source of local funding sources in the form that is with him reduce dependence on oil revenues to finance the general budget in Iraq, the risks and the study found a number of conclusions from the most important: that the corporate tax comes in the introduction to the components of the income tax structure in terms of relative importance and formed a revenue source of prime The gross proceeds of the income tax in Iraq, where it contributed to more than a quarter of that

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Publication Date
Sat Dec 28 2024
Journal Name
Journal Of Physical Education
The Effect of a Psychological Counseling Program to reduce irrational ideas and the causal attribution of the coaches of the gymnasium sports care center
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The research aimed to prepare a psychological counseling program for the coaches of the Sports Care Center in the gymnasium, and to learn about the impact of the psychological counseling program in reducing irrational ideas and causal attribution of the coaches of the Sports Talent Care Center in the gymnasium, to assume that there are statistically significant differences between the results of the tribal and posttests of the research group Experimental in the scale of irrational ideas, and there are statistically significant differences between the results of the tribal and posttests of the experimental research group in the scale of the causal attribution scale, The experimental approach was adopted by designing one experimental

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Publication Date
Thu Apr 18 2019
Journal Name
Al-kindy College Medical Journal
Evaluation of Ultrasonography in the Diagnosis of Acute Appendicitis with Histopathology as Gold Standard
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Background: Acute appendicitis is the most common surgical abdominal emergency with a life time prevalence of 1 to 7 individuals. Because the clinical diagnosis of acute appendicitis remains a challenge to surgeons, so different aids were introduced like different scoring systems, computer aided programs, ultrasonography, computerized tomography, Magnetic resonance imaging, Gastrointestinal tract contrast studies and laparoscopy to improve the diagnostic accuracy.

Objective: To evaluate ultrasound in the diagnosis of acute appendicitis in those patients clinically diagnosed with histopathology as gold standard.

Methods: A cross sectional study carried in Al-kindy Teaching

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Publication Date
Mon May 25 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation the effect of hyaluronic acid on bone healing process in rabbits (Immunohistochemical study for TGF-β)
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Background: Bone augmentation techniques are commonly employed in medical fields. This biomaterial system must be readily available, easily applicable by minimally-invasive technique and able to release an osteoinductive growth factor. Such a system will be able to engineer new bone formation locally at the site of injection. Hyaluronic acid has osteogenic potential that can be exploited not only for repairing bone defects but also for providing transplantable bone for the reconstruction of a variety of bone defects. The aims of this study were to evaluate the effects of Hyaluronic acid gel on bone healing by immunohistochemical estimation of transforming growth factor -beta 3 in experimental and control groups. Materials and methods: Thirt

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Publication Date
Mon May 25 2026
Journal Name
Journal Of Physical Education
The Study of Change Management Reality in Administrative Bureaus' Human resources for Some Baghdad Sports Clubs
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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Study the Relationship between Beta Decay Stability of Nuclide and its Shape for Some even-even Isobars
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The aim of this work is to learn the relationship of the stability of (β) emitter isobars with their shape for some isobaric elements with even mass number (A=152 - 162). To reach this goal firstly the most stable isobar have been determined by plotting mass parabola (plotting the binding energy (B.E) as a function of the atomic number (Z)) for each isobaric family. Then three-dimensional representation graphics for each nucleus in these isobaric families have been plotted to illustrate the deformation in the shape of a nucleus. These three-dimensional representation graphics prepared by calculating the values of semi-axis minor (a), major (b) and (c) ellipsoid axis’s. Our results show that the shape of nuclides which is represented the

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Publication Date
Sun Jul 22 2018
Journal Name
New Journal Of Chemistry
Jahn–teller distortion in 2-pyridyl-(1, 2, 3)-triazole-containing copper (II) compounds
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The syntheses, characterization and experimental solid state X-ray structures of five low-spin paramagnetic 2-pyridyl-(1,2,3)-triazole-copper compounds, [Cu(Ln)2Cl2], are presented in this study, for the following five Ln ligands: L1 = 2-(1-(p-tolyl)-1H-(1,2,3-triazol-4-yl)pyridine), L2 = 2-(1-(4- chlorophenyl)-1H-(1,2,3-triazol-4-yl)pyridine), L3 = 4-(4-(pyridin-2-yl)-1H-(1,2,3-triazol-4-yl)benzonitril), L4 = 2-(1-phenyl-1H-(1,2,3-triazol-4-yl)pyridine) and L5 = 2-(1-(4-(trifluoromethyl)phenyl)-1H-(1,2,3- triazol-4-yl)pyridine). These five [Cu(Ln)2Cl2] complexes each contain two bidentate 2-pyridyl-(1,2,3)- triazole (Ln) and two chloride ions as ligands, with the Cu–N(pyridine) bonds, Cu–N(triazole) and Cu–Cl bonds trans to each othe

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Publication Date
Sat Jan 01 2022
Journal Name
Proceeding Of The 1st International Conference On Advanced Research In Pure And Applied Science (icarpas2021): Third Annual Conference Of Al-muthanna University/college Of Science
Interleukin 2−330 single nucleotide polymorphism association with type 1 diabetes in Iraqi patients
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Type 1 diabetes (T1D) is an autoimmune disease with chronic nature resulting from a combination of both factors genetic and environmental. The genetic contributors of T1D among Iraqis are unexplored enough. The study aimed to shed a light on the contribution between genetic variation of interleukin2 (IL2) gene to T1D as a risk influencer in a sample of Iraqi patients. The association between IL2−330 polymorphism (rs2069762) was investigated in 322 Iraqis (78 T1D patients and 244 volunteers as controls). Genotyping for the haplotypes using polymerase chain reaction test – specific sequence primer (PCR-SSP) for (GG, GT, and TT) genotypes corresponding to (G and T) alleles were performed. A significant association revealed a decreased freq

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Publication Date
Mon May 01 2017
Journal Name
Spectrochimica Acta Part A: Molecular And Biomolecular Spectroscopy
Extraction, preparation and application of pigments from Cordyline fruticosa and Hylocereus polyrhizus as sensitizers for dye-sensitized solar cells
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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
Preparation and characterization of biomass-alumina composite as adsorbent for safranine-o dye from aqueous solution at different temperatures
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