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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
Wed Apr 25 2012
Journal Name
Journal Of Chromatographic Science
Direct Acetylation and Determination of Chlorophenols in Aqueous Samples by Gas Chromatography Coupled with an Electron-Capture Detector
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A method was developed that offers a rapid, simple and accurate technique for the determination of chlorophenols at trace levels in aqueous samples with very limited volumes of organic solvents. These compounds were acetylated, then preliminarily extracted with n-hexane. The enriched chlorophenols were directly analyzed using gas chromatography with an electron-capture detector. The detection limits were in the range of 0.001–0.005 mg/L, except for 2-chlorophenol, which was always above 0.013 mg/L. Relative standard deviation for the spiked water samples ranged from 2.2 to 6.1%, while relative recoveries were in the range of 67.1 to 101.3%.

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Microscopic effective charges and quadrupole moments of sd-shell and sd-pf cross-shell nuclei with Z≥13
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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Synthesis, Characterisation and Biological Activity of New Co, Ni, Zn and Cd Polymeric Complexes Derived from Dithiocarbamate Ligand
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Synthesis of a new class of Schiff-base ligand with a tetrazole moiety to form polymeric metal complexes with CoII, NiII, ZnII, and CdII ions has been demonstrated. The ligand was synthesised by a multi-steps by treating 5-amino-2-chlorobenzonitrile and cyclohexane -1,3-dione, the 5,5'-(((1E,3E)-cyclohexane-1,3-diylidene)bis(azanylylidene))bis(2-chlorobenzonitrile) was obtained. The precursor (M) was prepared  from the reaction 5,5'-(((1E,3E)-cyclohexane-1,3-diylidene)bis(azanylylidene))bis(2-chlorobenzonitrile) with NaN3 to obtained (1E,3E)-N1,N3-bis(4-chloro-3-(1H-tetrazol-5-yl)phenyl)cyclohexane-1,3-diimine (N). By reacting the precursor (M) with CS2

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Publication Date
Sat Mar 05 2022
Journal Name
Mathematical Methods In The Applied Sciences
Double‐diffusive convection on peristaltic flow of hyperbolic tangent nanofluid in non‐uniform channel with induced magnetic field
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Consequence of thermal and concentration convection on peristaltic pumping of hyperbolic tangent nanofluid in a non‐uniform channel and induced magnetic field is discussed in this article. The brief mathematical modeling, along with induced magnetic field, of hyperbolic tangent nanofluid is given. The governing equations are reduced to dimensionless form by using appropriate transformations. Exact solutions are calculated for temperature, nanoparticle volume fraction, and concentration. Numerical technique is manipulated to solve the highly non‐linear differential equations. The roll of different variables is graphically analyzed in terms of concentration, temperature, volume fraction of nanoparticles, axial induced magnetic fie

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Publication Date
Wed Jun 01 2022
Journal Name
Baghdad Science Journal
Estimation of Radiation Dose from Most Common Pediatrics Radiographic Examinations within Main Central Hospitals in Najaf City, Iraq
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In this study the Entrance Surface Dose (ESD) received by pediatrics patients undergoing chest, abdomen and skull X-ray examinations was estimated. The study was conducted in two hospitals in Najaf city where three radiographic systems were considered. The study participants were classified into four age groups 0-1 ,  1-5 ,  5-10  and  10-15  years. Calculations were performed using exposure factors, kVp, mAs and focal-skin distance, together with patient data age. The ESD was calculated for the involved patients who underwent an Antero-posterior (AP) chest, abdomen and skull X-ray examination. The resulted data were analyzed and compared with international dose references. For all studied radiographic examinations and all X-ray mac

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Publication Date
Thu Feb 01 2024
Journal Name
Biologicals
Adjuvant effects of novel water/oil emulsion formulations on immune responses against infectious bronchitis (IB) vaccine in mice
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Publication Date
Wed Mar 05 2025
Journal Name
Bulletin Of The Chemical Society Of Ethiopia
Synthesizing, characterization of some metal ion complexes with new azo dye and studying antioxidant and anticancer (MCF-7)
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This new azo dye 7-(3-hydroxy-phenylazo)-quinoline-8-ol was subsequently used to prepare a series of complexes with the chlorides of Fe, Co, Zn, Ru, Rh and Cd. The compounds identified by 1H and 13C-NMR, FT-IR, UV-Vis, mass spectroscopy, as well as TGA, DSC, and C.H.N., conductivity, magnetic susceptibility, metal and chlorine content. The results showed that the ligand behaves in a trigonal behavior, and that the complexes gave tetrahedral, except for Fe, Ru and Rh octahedral was given, that all of them are non-electrolytes. The effectiveness of both the compounds in inhibiting free radicals was evaluated by the ability to act as an antioxidant was measured using DPPH as a free radical and gallic acid as a standard substance, the

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Physics: Conference Series
Effect of Nickel Substitution On Structural and Electrical Properties of Hg<sub>0.5</sub>Pb<sub>0.5</sub>Ba<sub>2</sub>Ca<sub>2</sub>Cu<sub>3-y</sub>Ni<sub>y</sub>O<sub>8+δ</sub> Superconductor Composite
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Abstract<p>six specimens of the Hg<sub>0.5</sub>Pb<sub>0.5</sub>Ba<sub>2</sub>Ca<sub>2</sub>Cu<sub>3-y</sub> <italic>Ni<sub>y</sub> </italic>O<sub>8+δ</sub> (y=0.2,0.4,0.6,0.8,1.0) superconducting compound were prepared by solid state reaction method, with sintering temperature equal to 1123K for 24 hours. The electrical resistivity was examined by the four probe technique, It was found that all the specimens have metallic behavior and increasing the critical temperature with increasing nickel concentration. The optimum critical temperature T<sub>c</sub> was found equal </p> ... Show More
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Publication Date
Mon May 01 2017
Journal Name
The Journal Of Immunology
Protective effects of Δ9-Tetrahydrocannabinol (THC) results from alteration in lung dysbiosis mediated by SEB-induced acute lung injury
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Abstract<p>Inhalation of Staphylococcal Enterotoxin B (SEB) is known to induce acute lung injury (ALI) and studies from our laboratory have shown that THC, a psychoactive ingredient found in Cannabis sativa, can attenuate the ALI. In the current study, we investigated the role played by lung microbiota in ALI with or without THC treatment. A dual-dose of SEB was given to C3H/HeJ mice, which were then treated either with vehicle or THC. SEB-administration caused ALI and 100% mortality while all THC-treated mice survived and suppressed the inflammation in the lungs. Furthermore, lung microbiota was collected and 16S rRNA sequencing was performed. The data were analyzed to determine the alpha and b</p> ... Show More
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Publication Date
Mon Mar 15 2021
Journal Name
Iraqi National Journal Of Nursing Specialties
Effect of Pioneer Aeromedical Evacuation Program on Flight Medics' Knowledge toward Emergency Casualties at Army Aviation Bases in Iraq
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Objective(s): The aims of present study to findout the effect of aeromedical evacuation program on flight medics’ knowledge.
Methods: A pre-experimental design is carried in army aviation bases in Iraq, for the period of April 1st 2019 to October 25th 2019. Non-probability "purposive" sample of (30) flight medics are selected from army aviation bases. The questionnaire consisted of two main parts: the demographic characteristics of air paramedics, and the second part included five axes, which are (50) paragraphs related to the knowledge of air paramedics towards emergency injuries. The researcher used the statistical program version 20 to analyze the data, and the stability of the questionnaire was measured through the pre and post

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