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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 Dec 28 2020
Journal Name
The Iraqi Journal Of Veterinary Medicine
Isolation and Molecular Identification of Nontuberculous Mycobacterium from Different Species of Fish in Karbala Province, Iraq
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This study was designed for isolation and molecular identification of Nontuberculous Mycobacterium (NTM) from fish during the period between October and December 2017 from Karbla province, Iraq. This study included 200 fresh fish samples from four different species including Spondyliosoma cantharus, Liza abu, Carassius carassius and Cyprinuscarpio. Three samples of each fish were taken including gills, muscles and all internal organs. The samples were processed by decontamination, concentration of 4% sodium hydroxide, and 0.1 ml of sediment was streaking on Löwenstein Johnson (LJ) media; then the bacterial cultures were incubated at 28-30 °C for 3days up to 4 weeks and suspected colonies were stained with acid fast stain to confir

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Publication Date
Sun Dec 01 2019
Journal Name
Baghdad Science Journal
Molecular Identification of Fusobacterium Isolates and limitation of Biofilm Formation Adhesion Gene (fadA) in Dental Outpatients
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 Fusobacterium are compulsory anaerobic gram-negative bacteria, long thin with pointed ends, it causes several illnesses to humans like pocket lesion gingivitis and periodontal disease; therefore our study is constructed on molecular identification and detection of the fadA gene which is responsible for bacterial biofilm formation. In this study, 10.2% Fusobacterium spp. were isolated from pocket lesion gingivitis. The isolates underwent identification depending on several tests under anaerobic conditions and biochemical reactions. All isolates were sensitive to Imipenem (IPM10) 42.7mm/disk, Ciprofloxacin (CIP10) 27.2mm/disk and Erythromycin (E15) 25mm/disk, respectively. 100% of

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Publication Date
Mon Jun 26 2023
Journal Name
Journal Of Contemporary Medical Sciences
Molecular detection of mononucleotide biomarkers of microsatellite instability in sporadic colorectal carcinoma patients with clinicopathological correlation
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Objectives: To identify the frequency and types of microsatellite instability among a group of sporadic CRC patients and to correlate the findings with clinicopathological characteristics. Methods: During an 8-month period, all patients with sporadic CRC who attended to two teaching hospitals in Baghdad, Iraq were recruited to this cross-sectional study regardless of age, sex, ethnicity, or tumor characteristics. Demographic, clinical, and histopathological features were recorded. DNA was extracted from FFPE-blocks of the resected tumors and normal tissues. PCR amplification of five microsatellite mononucleotide repeat loci (BAT25, BAT26, NR-21, NR-24, and MONO-27) and 2 pentanucleotide repeat control markers (Penta C and Pent

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Publication Date
Wed Jul 13 2022
Journal Name
International Journal Of Health Sciences
Study of the reliability of serum vascular endothelial growth factor and its soluble receptor as markers of diabetic nephropathy in type 2 diabetes patients
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The levels of circulating angiogenic and anti-angiogenic factors, namely vascular endothelial growth factor–A (VEGF-A) and soluble vascular endothelial growth factor receptor-1 (sVEGFR-1), have been linked to the development of renal dysfunction due to the proliferation of microvasculature within the kidneys of type 2 diabetic (T2DM) patients. The study aims to scrutinize serum levels of VEGF and sVEGFR-1 in a sample of Iraqi diabetic nephropathy patients to support their reliability as markers for the prediction of nephropathy in type 2 diabetes mellitus patients as well as to assess the ACE inhibitor’s effect on the levels of these two markers. Method: The ninety participants of this case-control study were split into three gr

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Publication Date
Wed Nov 26 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Measurement of salivary Immunoglobulin A of participants with a healthy, gingivitis and chronic periodontitis conditions
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Background: Secretory Immunoglobulin A (SIgA) is a subclass of Immunoglobulin A (IgA), It is an antibody that plays an important role in mucosal immunity. It is the main immunoglobulin found in mucous secretions from mammary glands, tear glands and salivary glands, every pathologic process in the body involves the immune system, and periodontal inflammation is one of them and is not an exception. Material and methods: this study was consisted of 60 healthy male participants of an age ranged between (35-50) years old ; 25 of them with generalized moderate chronic periodontists(Clinical Attachment Loss equal to 3-4mm at ≥ 30% of the sites; 20 participants with plaque induced gingivitis and 15 participants had clinically healthy pe

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Publication Date
Mon Mar 23 2020
Journal Name
Journal Of Engineering
Experimental Investigation of Thermal Performance of a Solar Chimney Provided with a Porous Absorber Plate
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Experimental investigation of the influence of inserting the metal foam to the solar chimney to induce natural ventilation are described and analyzed in this work. To carry out the experimental test, two identical solar chimneys (without insertion of metal foam and with insertion of metal foam) are designed and placed facing south with dimensions of length× width× air gap (2 m× 1 m× 0.2 m). Four incline angles are tested (20o,30o,45o,60o) for each chimney in Baghdad climate condition (33.3o latitude, 44.4o longitude) on October, November, December 2018. The solar chimney performance is investigated by experimentally recording absorber pl

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of The College Of Languages (jcl)
A comparative reading of the social and political satire in the works of Abu al-Fadl Zrui Nasrabad and Ahmad Rajab (The tadhk: خوانش تطبیقی طنز اجتماعی – سیاسی در آثار ابوالفضل زرویی نصرآباد و احمد رجب(مورد مطالعه: تذکرة المقامات زرویی و نصف كلمة احمد رجب)
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           Satire is genre of the literary arts that has always been the source of human interest. Because  it is difficult to accept direct criticism, Satire appears as a literary tool in which vices, follies, abuses and shortcomings are held up to ridicule, with the intent of shaming individuals, corporations, government, or society itself into improvement. A satirical critic usually employs irony to attain this goal. Although satire is usually meant to be humorous, its greater purpose is often profitable social criticism, using wit to draw at

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Publication Date
Wed Aug 31 2022
Journal Name
Sciencerise: Pharmaceutical Science
The morphological analysis of crystalline methadone: a novel combination of microscopy techniques
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The aim: to evaluate combined microscopy techniques for determining the morphological and optical properties of methadone hydrochloride (MDN) crystals. Materials and methods: MDN crystal formation was optimized using a closed container method and crystals were characterized using polarized light microscope (PLM), scanning electron microscopy (SEM) and confocal microscopy (CM). SEM and CM were used to determine MDN crystal thickness and study its relationship with crystal retardation colours using the Michel-Levy Birefringence approach. Results: Dimensions (mean±SD) of diamond shaped MDN crystals were confirmed using SEM and CM. Crystals were 46.4±15.2 Vs 32.0±8.3 µm long, 28.03±8.2 Vs 20.85±5.5 µm wide, and 6.62±

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Publication Date
Thu Nov 02 2023
Journal Name
Journal Of Engineering
Numerical Simulation of the Thermal Performance of a Tubular Solar Air Heater
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In this work, a flat-plate solar air heater (FSAH) and a tubular solar air heater (TSAH) were designed and tested numerically. The work investigates the effect of increasing the contact area between the flowing air and the absorber surface of each heater and predicts the expected results before the fabrication of the experimental rig. Three-dimensional two models were designed and simulated by the ANSYS-FLUENT 16 Program. The solar irradiation and ambient air temperature were measured experimentally on December 1st 2022, at the weather conditions of Baghdad City- Iraq, at three air mass flow rates, 0.012 kg/s, 0.032 kg/s, and 0.052 kg/s. The numerical results showed the advantage in the thermal performance of

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Publication Date
Tue Sep 30 2014
Journal Name
Iraqi Journal Of Science
The Prevalence of Autoimmune Thyroiditis in A sample of Infertile Iraqi Women
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In the present study, the aim was made to identify the relationship between thyroid autoimmunity (TAI) and female infertility. The study was performed on 30 infertile women and 22 age-matched healthy fertile control age (33 ± 5 years). Overall, serum prolactin (PRL), thyroid stimulating hormone (TSH) assay is the key test for the diagnosis and management of hypo and hyperthyroidism. Anti-TPO Ab and anti-TG Ab were measured. The mean ± SE of serum PRL (31.080 ± 3.06) ng/ml was significantly (P<0.05) higher in infertile group compared with control (16.191±1.36) ng/ml. Serum TSH was significantly (P<0.05) higher in infertile group (5.689 ± 1.12) µIU/ml compared to control group (2.282 ± 0.18) µIU/ml. The prevalence of positive

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