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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 Apr 30 2024
Journal Name
International Journal Of Phytopathology
Role of Arbuscular Mycorrhiza (AM) Fungi and Lignin in Biological Control against Vascular Fusarium Wilt Disease
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The current study aimed to assess the biological efficacy of the triple arbuscular mycorrhiza (AM) mixture of fungi Glomus etunicatum, G. leptotichum and Rhizophagus intraradices, and mix it with organic matter (O) and pathogenic fungi Fusarium oxysporum f.sp.lycopersici by using voyeurism in the plastic house in the growth of the tomato plant after four and eight weeks of cultivation. The results were shown after the treatment of the tomato plant in agriculture with the mixture of mycorrhiza and the pathogenic fungi and organic matter were treated with the mixture of mycorrhiza, organic matter and pathogenic fungi together. The effect of mycorrhiza and organic matter interference on the increase in the percentage of the lignin afte

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Publication Date
Mon Feb 04 2019
Journal Name
Iraqi Journal Of Physics
Structure dependence of gamma ray irradiation effects on polyurethane and epoxy resin studied by PAL technique
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Positron annihilation lifetime (PAL) technique has been employed to
study the microstructural changes of polyurethane (PU), EUXIT 101
and epoxy risen (EP), EUXIT 60 by Gamma-ray irradiation with the
dose range (95.76 - 957.6) kGy. The size of the free volume hole and
their fraction in PU and EP were determined from ortho-positronium
lifetime component and its intensity in the measured lifetime spectra.
The results show that the irradiation causes significant changes in the
free volume hole size (Vh) and the fractional free volume (Fh), and
thereby the microstructure of PU and EP. The results indicate that
the γ-dose increases the crystallinity in the amorphous regions of PU
and increas

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Publication Date
Fri Sep 27 2019
Journal Name
Journal Of Baghdad College Of Dentistry
Clinical Assessment and Cytomorphometric Analysis of Buccal Mucosal Cells in Behçet’s Disease Patients
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Background: Behçet’s disease (BD) is a disorder of systemic inflammatory condition. Its important features are represented by recurrent oral, genital ulcerations and eye lesions. Aims. The purpose of the current study was to evaluate and compare cytological changes using morphometric analysis of the exfoliated buccal mucosal cells in Behçet’s disease patients and healthy controls, and to evaluate the clinical characteristics of Behçet’s disease. Methods. Twenty five Behçet’s disease patients have been compared to 25 healthy volunteers as a control group. Papanicolaou stain was used for staining the smears taken from buccal epithelial cells to be analyzed cytomorphometrically. The image analysis sof

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Publication Date
Fri Jun 01 2012
Journal Name
J Med J
Relationship of seminal biochemical parameters and serum reproductive hormones with sperm function tests in asthenospermic patients
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Aim: The aim of this study is to determine the correlation between levels of certain seminal biochemical parameters and serum reproductive hormones, on the one hand, and sperm function tests, on the other hand, in asthenospermic patients. Patients and Methods: Sixty asthenospermic patients and twenty fertile men as a control group were included in this study. Semen samples were collected to perform seminal fluid analysis. Total protein, cholesterol, calcium, creatine kinase, and fructose were measured in the seminal plasma. Blood samples were collected for hormonal assay of serum reproductive hormones: testosterone, prolactin, luteinizing hormone, and follicle-stimulating hormone. Results: The results revealed a significant positive correla

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Publication Date
Fri Jul 26 2024
Journal Name
Proceeding Books
 Impact of Do It Yourself (DIY) Strategy on Fifth Preparatory School Pupils’ Achievement in Reading Comprehension
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The primary objective of this study is to examine the effects of a do-it-yourself (DIY) technique on the reading comprehension performance of fifth-grade students in preparatory schools. In order to accomplish the objective of this research, it is posited that a null hypothesis can be established, suggesting that there are no statistically significant disparities between the average scores of the experimental group, which is instructed using a do-it-yourself (DIY) strategy, and the control groups, which are instructed using a prescribed method, in terms of their reading comprehension attainment. Developing a pre- and post-achievement test. Both groups have been equalized in terms of characteristics such as parental educational leve

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Publication Date
Mon Dec 23 2019
Journal Name
Modeling Earth Systems And Environment
Facies architecture and stratigraphic sequence of Zubair Formation in Majnoon and Suba oil fields, Southern Iraq
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Publication Date
Sat Jun 30 2012
Journal Name
Al-kindy College Medical Journal
Erythrocyte Magnesium Levels in type I and type II Iraq diabetic patients effect of antidiabetic treatment
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Background: Direct measurement of intracellular magnesium using erythrocytes has been suggested as a sensitive indicator for the estimation of body magnesium store. Marked depletion in plasma and erythrocyte magnesium levels was particularly evident in diabetic patients with advanced retinopathy and poor diabetic control. While insulin has been shown to stimulate erythrocyte magnesium uptake, hyperglycemia per se suppressed intracellular magnesium in normal human red cells.
Aim of the study: To investigate the erythrocyte magnesium level in Iraqi type I and II diabetic patients, with specific emphasis on the effect of both, metabolic control and the type of antidiabetic treatments.
Methods: Sixty two diabetic patients (7 with type

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Publication Date
Tue Sep 01 2009
Journal Name
Al-khwarizmi Engineering Journal
Corrosion and Galvanic behavior of Copper, Carbon steel and Zinc Couples in (3.5 %wt) Nacl Solution
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The galvanic corrosion of the (Cu - Fe), (Cu - Zn) and (Fe - Zn) couples have been investigated in 3.5% NaCl solution, 40ºC, different velocities (Re = 5000, 10000 and 15000) and different area ratio’s of cathode to anode (AR= 0.5,1 and 2), by using commercial metal pipe (cylindrical tube).The Zero Resistance Ammeter has been used to measure the galvanic current (Ig) and galvanic potential (Eg) with time. The galvanic current density increases with increasing velocity (Re) and the area ratio (AR). The galvanic potential (Eg) is shifted to less negative with increasing velocity (Re) and the area ratio (AR). A statistical relations for the galvanic current density and galvanic potential as a function of (Re). and the area ratio had been

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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of The Mechanical Behavior Of Materials
Residual strength and strengthening capacity of reinforced concrete columns subjected to fire exposure by numerical analysis
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Abstract<p>This study is a numerical investigation of the performance of reinforced concrete (RC) columns after fire exposure. This study aims to investigate the effect of introducing lateral ties and using the RC jacket on improving post-fire behavior of these columns, the effect of the duration of the fire on ultimate load of columns. The analysis was performed through ABAQUS, a 3D – non-linear finite element program. 4 m tall lengthening square RC column with a cross- section of 0.4 m × 0.4 m was used as a test specimen. The RC column was reinforced by 4Ø28 mm longitudinal bars bonded by steel tie bars of Ø10 mm spaced at 400 mm. The firing temperature was increased to 60</p> ... Show More
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Publication Date
Wed Jul 01 2020
Journal Name
The Iraqi Postgraduate Medical Journal
Prevalence and Risk Factors of Low Birth Weight in Al- Elwiya Maternity Teaching Hospital in Baghdad
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