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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
Sun Mar 13 2011
Journal Name
Baghdad Science Journal
Effect of Phoenix dactylifera pollen grains suspension on spermatogenesis and some biochemical parameters in albino rats
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In this study forty mature albino rats were used wich were randomly divided into five groups ,four groups were adminstrated Phoenix dactylifera pollen grains suspension at concertenrations (18,54,108,and 216)mg/ kg body weight by oral administration while the fifth group was considered as a control group.Experiment continued for 40 days then rats were sacrificed and samples of blood were collected for determination of some biochemical parameters (total protein ,total cholesterol ,LDLc and HDLc).Testis were removed for preparation histological sections to measures the diameters of seminferous tubules ,thickness of seminiferous epithelium and the numbers of spermatogenic cells.

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Publication Date
Mon Jun 10 2019
Journal Name
Journal Of Global Pharma Technology
Mixed Ligand Schiff Base Complexes of Some Meta(II) Salts: Preparation. Spectral Characterization and Antibacterial Screening
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FH Ghanim, Journal of Global Pharma Technology, 2018

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Publication Date
Thu Dec 01 2022
Journal Name
Journal Of Chemical Health Risks
Preparation, Characterization and Antibacterial Activity of some New Oxazolidin-5-one Derivatives Derived from Imine Compounds
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In this research, 5- membered heterocyclic compounds as oxazolidine-5-one J1-J5 derivatives were prepared using primary aromatic amine, aromatic carbonyl compounds and chloroacetic acid. By combining primary aromatic amines and aromatic carbonyl compounds, Schiff's bases were synthesized. Schiff bases are used with the chloroacetic acid compound to prepare oxazolidine-5-one J1-J5 derivatives. The compounds J1-J5 were described using NMR spectroscopy and FT-IR. .The biological efficacy was evaluated according to maximum inhibitory concentrations (MICs) toward Staphyloccoccus aureus and Esherichia coli. The best MIC was 210 μg ml-1 for J4 against the two pathogenic bacteria, while J1, J4, and J1 did not show any inhibitory effect against all

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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Analysis and Control of PWM Buck-Boost AC Chopper Fed Single-Phase Capacitor Run Induction Motor
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Single phase capacitor-run induction motors (IMs) are used in various applications such as home appliances and machine tools; they are affected by the sags or swells and any fault that can lead to disturb the supply and make it produce rms voltage below or above the rated motor voltage, which is 220V. A control system is designed to regulate the output voltage of the converter irrespective to the variation of the load and within a specific range of supply voltage variation. The steady-state equivalent circuit of the Buck-Boost chopper type AC voltage regulator, as well as the analysis of this circuit are presented in this paper. Switching device for the regulator is an IGBT Module. The proposed chopper uses pulse width modulation (PWM) c

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Publication Date
Thu Aug 21 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Histological and histomorphometric analysis of strontium chloride coated commercially pure titanium implant compared with hydroxyapatite coating
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Background: In recent years, the immediate loading of dental implants has become more accepted as a standard protocol for the treatment of the edentulous area. Success in implant dentistry depends on several parameters that may improve phenomenon of osseointegration and new bone formation in close contact with the implant. The aim of study was to evaluate the effect of strontium chloride coating of screw shape commercially pure titanium dental implant osseointegration at bone - implant interface by histomorphometric analysis and compare with hydroxyapatite coating at 2 time periods (2 weeks and 6 weeks). Materials and methods: Electrophoretic Deposition Technique (EPD) was used to obtain a uniform coating layer on commercially pure titanium

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Publication Date
Sun Sep 22 2019
Journal Name
International Journal Of Pharmaceutical Research
Synthesis, Characterization and Antibacterial of Some New 4,4'-(pyridine-2,6-diylbis(1,3,4- oxadiazole-5,2-diyl))bisphenolPolymer
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4,4'-(pyridine-2,6-diylbis(1,3,4-oxadiazole-5,2-diyl))bisphenol monomer (3)was synthesized from cyclization of N'2,N'6-bis(4-hydroxybenzylidene)pyridine-2,6-dicarbohydrazide (2)in the presence of bromine in glacialacetic acid. Newly five polymers (P1-P5) were synthesized from reaction bis-1,3,4-oxadiazole bisphenolmonomer with five different di acid chloride. The antibacterial activity of the synthesized polymers was screened against gram positive and gram negative bacteria. Polymers P4 and P5 exhibited significant antibacterial against all microorganisms, as well these polymers showed highest antifungal activity.

Publication Date
Wed Apr 01 2020
Journal Name
Indian Journal Of Forensic Medicine & Toxicology
Evaluation of some inflammatory cytokines and glycated hemoglobin in uncontrolled type 2 diabetes mellitus with nephropathy
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Background: Chronic hyperglycemia causes diabetic nephropathy(DN), which is a typical microvascular complication of type 2 diabetes mellitus. The pathogenesis of DN is not fully understanding. The inflammation may possess a significant role in the progression of DN in diabetic patients. Method: The study accomplished at teaching laboratories of medical city, Baghdad, Iraq. It was included 50uncontrolled diabetic type 2 patients with nephropathy, age range (40-78) years and 42 controlled diabetics type 2 without nephropathy, age range (35 - 52) years as a control group. The participants divided in to two groups according to HbA1c measurement which is described as follows: < 7.5% of HbA1c describes controlled diabetes, and > 9% of HbA1c

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Publication Date
Fri Dec 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Color stability of nano resin-modified glass Ionomer restorative cement after acidic and basic medications challenge
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Background: Color stability of glass ionomers (GIs) could be affected by many factors such as pH and consumption of liquid medications like antibiotics. Most common antibiotics used during childhood are amoxicillin suspension (AM.S) and azithromycin suspension (AZ.S) which have acidic and basic pH respectively. Aim: to evaluate and compare the effect of AM.S and AZ.S on color stability of nano resin-modified GI. Methods: Thirty disc of nano resin-modified glass ionomer (2mm height x 4mm diameter) were divided into three groups (n=10 for each) and independently exposed to AM.S, AZ.S, and artificial saliva (A.S.). Color stability was evaluated in triplicate by VITA Easyshade® before and after three immersion protocols, repeated over a thr

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Publication Date
Tue Jun 01 2021
Journal Name
Baghdad Science Journal
Incidence of intestinal parasitic infections among random samples at Al- Aziziyah hospital in Wasit province/Iraq
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     The study is designed to identify intestinal parasitic infections examined at Al-Aziziyah Hospital in Wasit Governorate in Iraq. In this study, a total of (460) internal and external patients were monitored for intestinal parasitic infections. All stool samples were analyzed by the direct method (microscopic exam.) to discover the trophozoite stages and cyst stages for intestinal protozoan parasites. The most incidence parasites in different sex, area residence and different age groups. Out of (460) patient sample were infected with 217 at a percentage of (47.17%), 101(46.5%) were for males and 116 (53.5%) were for females. It was found that the numbers and percentages of a single (one

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Physics: Conference Series
Theoretical Discussion of Electron Transport Rate Constant at TCNQ / Ge and TiO<sub>2</sub> System
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