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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
Thu Nov 07 2024
Journal Name
Journal Of Thermal Analysis And Calorimetry
Performance improvement of phase change material (PCM)-based shell-and-tube-type latent heat energy storage system utilizing curved fins
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Publication Date
Wed Jun 16 2021
Journal Name
Biochemical And Cellular Archives
Synthesis, characterization and pharmaceutical studies of schiff base from 2-pyrrolidinone derivative and imidazole-2-carboxaldehyde and corresponding complexes with Metal (||)
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Synthesis, characterization and pharmaceutical studies of schiff base from 2-pyrrolidinone derivative and imidazole-2-carboxaldehyde and corresponding complexes with Metal (||)

Publication Date
Sun Mar 01 2020
Journal Name
Baghdad Science Journal
Evaluation of Sex Hormone Levels in Benign Prostatic Hyperplasia Patients Treated with 5 Alpha-Reductase Inhibitor (Finasteride) in Amara city/Iraq
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The present study aimed to determine the serum sex hormone levels among Benign Prostatic Hyperplasia (BPH) patients before and after 3 months of oral administration of 5-α reductase inhibitor(finasteride). Forty BPH patients and 40 healthy men from Amara city were involved in this study, their ages were between 40-59 year. They were all subjected  to direct estimation of hormones by MinVidas method including Testosterone (T), Estradiol (E2), Follicle Stimulating Hormone (FSH), Luteinizing Hormone (LH), Prolactin (PRL), and Dihydrotestosterone (DHT) before and after 3 months of treatment with 5α-reductase inhibitor (finasteride) (the healthy individuals didn’t take finasteride).The results showed that T level was significantly lo

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Publication Date
Sun Mar 02 2014
Journal Name
Baghdad Science Journal
Inhibition activity of Saccharomyces boulardii and Lactobacillus acidophilus against pathogenic E.coli isolates from Recurrent Urinary Tract Infection in women In Vitro
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The aims of study is to detect the inhibitory effect of Saccharomyces boulardii and Lactobacillus acidophilus on Escherichia coli that has been isolated from recurrent urinary tract infection in women. The sensitivity of E.coli isolates to antibiotics had been studied and the most resistant E.coli isolate to antibiotics had been studied .The cup assay was used on nutrient agar and Muller-Hinton agar to detect the inhibitory activity for each S.boulardii yeast grown on YEGP media and L.acidophilus grown on MRS media in which the result showed a high inhibition activity for each of them .Also in this study the adhesion property of E.coli had been evaluated in the presence of S.boulardii at concentration of 1×109 and L.acidophilus at conc

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Publication Date
Tue Nov 11 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal health status in relation to physicochemical characteristics of saliva among pre-menopausal and post-menopausal women in Baghdad city-Iraq
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Background: Menopause can bring oral health problems and also associated with significant adverse changes in the orofacial complex. After menopause, women become more susceptible to periodontal disease due to deficiency of estrogen hormone. Current study aimed to evaluate the periodontal health status in relation to salivary constituent including pH, flow rate and some elements (Magnesium, Calcium and inorganic phosphorus) of pre and post-menopause women. Materials and Methods: Periodontal health status of 52 women aged 48-50 years old (26 pre-menopause and 26 post-menopause) were examined including (gingival index, plaque index, calculus index, probing pocket depth and clinical attachment level). Salivary sample was collected for two women

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Publication Date
Sun Mar 01 2020
Journal Name
International Journal Of Pharmaceutical Research
Phytochemical investigation,anti-proliferative and antioxidant- activities of Iraqi Capparisspinosa L. (Family Capparidaceae) against MCF-7 human Breast cancer cell line
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Publication Date
Sun Sep 01 2019
Journal Name
Meta Gene
Association of HLA-G + 3142G > C gene polymorphism and toll-like receptor-9 serum level in systemic lupus erythematosus patients
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Background: Human leukocyte antigen-G (HLA-G)and Toll-like receptor-9 (TLR-9)play a role in the regulation of autoimmune diseases and inflammatory processes. Aim of the study: To detect the HLA-G + 3142G > C gene polymorphism that associated with the susceptibility to SLE patients and associated with Hepatitis B infection and TLR-9 serum level. Patients and methods: This study was done on 75 SLE patients and 75 healthy control groups. Genotyping of HLA-G + 3142G > C were detected by PCR and PCR-RFLP methods. In addition to the estimation of Hepatitis B surface (HBs)antigen status by immunochromatography technique and TLR-9 serum level by ELISA technique. Results: The HLA-G + 3142G > C gene polymorphism between the SLE patients and controls

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Publication Date
Sat Dec 11 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Ameliorative Role of Nutraceutical Quercetin and its Derivatives Against Cognitive Impairment Process Induced by Lead Exposure in Drosophila melanogaster(Fruit Fly)
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Cumulative lifetime lead (Pb) exposure has been associated with accelerated declines in cognition through the free radical generation and epigenetic effects. Several pieces of literature have identified a correlation between exposure to lead and neurodegenerative disorders. Harwich strain Drosophila melanogaster was exposed to lead acetate for two weeks, and changes in pulse transmission by acetylcholinesterase and systemic redox were evaluated. Besides, molecular docking studies of acetylcholinesterase against Quercetin and its most common derivatives contained in food have been performed. Pharmacokinetic studies on Quercetin and its derivatives have also been performed in silico toxicity. The data obtained showed alterations in antioxi

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Publication Date
Wed Apr 19 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Synthesis and Spectral Studies of Some Metal Complexes with Bis[O,O-2,3;O,O-5,6(Chlorocarboxylic Methyliden)] L-Ascorbic Acid
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 The reaction of L-ascorbic acid with the tirchloroacetic acid in the presence of potassium hydroxide gave new product Bis[O,O-2,3;O,O-5,6(chlorocarboxylicmethyliden)]Lascorbic acid (H2L) which was isolated and characterized by 1H,13C-NMR, elemental analysis (C,H,N), UV-Visible and Fourier Transform Infrared (FTIR). The complexes of the ligand (H2L) with metal ions, M+2= (Cu, Co, Ni, Cd and Hg) were synthesized and characterized by FTIR, UV-Visible, molar conductance, atomic absorption, magnetic susceptibility and the molar ratio. The analysis evidence showed the binding of the metal ions with (H2L) through the bicarboxylato group manner resulting in six-coordinated metal ion. The TLC for (H2L) and complexes showed one spot for eac

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
Electrical Dielectric Authorship of Polyvinyl-Acetate and Toluene Diisocyanate (PVA-TDI) with Manufactured Sulfonated Phenol-formaldehyde (SPF) Viscous Mass Material Composite
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The electrical insulation of the manufacture sulfonated phenol-formaldehyde viscous material (product) has been studied with Polyvinyl-acetate (PVA) and toluene diisocyanate (TDI) blend has been prepared by fixing percentage by weight 3:1 and mixed with different percentages by weight of the product sulfonated phenol formaldehyde viscous mass (SPF). The Fourier transform infrared (FTIR) spectroscopy is done on (SPF) resin powder and prepared film of PVA-TDI-SPF viscous mass. The quality factor (Q), dissipation factor (D), parallel resistance (Rp), series resistance (Rs), parallel capacitance (Cp), series capacitance (Cs) and phase shift (?) are measured. The calculated maximum dielectric constant (??) is 3.49x107 at sample (1) wt.1% SPF vis

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