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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 Apr 29 2024
Journal Name
Journal Of The College Of Basic Education
Detection Of Biofilm Formation By Beta- Lactam Resistance Klebsiella Pneumoniae Isolated From Clinical Specimens And Aquatic Samples
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Publication Date
Mon Dec 20 2021
Journal Name
Baghdad Science Journal
Isolation and identification of some bacterial isolates from soil contaminated with crude oil and Testing Their Effectiveness
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Bacterial strains were isolated from oil-contaminated soil, in 2018, these isolates were identified, and with the aim of finding out the ability of these isolates to degrede the oil compounds, the color change of medium which added to it isolates was read by the method of Pacto Bushnell Hans. Then the change in the petroleum compounds was read by gas chromatography, for the most effective isolates.

The nine isolated bacterial showed different degrees of color change, and the isolates (Pseudomonas, Bacillus, Micrococcus) outperformed the color change amount (78, 78, 77) %, respectively, compared to the control, and the three isolates together showed the best color change of 90.7. % Compared to the control, and the

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Publication Date
Sun Jan 01 2023
Journal Name
Journal Of The Mechanical Behavior Of Materials
Transient response and performance of prestressed concrete deep T-beams with large web openings under impact loading
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Abstract<p>This study reports testing results of the transient response of T-shape concrete deep beams with large openings due to impact loading. Seven concrete deep beams with openings including two ordinary reinforced, four partially prestressed, and one solid ordinary reinforced as a reference beam were fabricated and tested. The effects of prestressing strand position and the intensity of the impact force were investigated. Two values for the opening’s depth relative to the beam cross-section dimensions were inspected under the effect of an impacting mass repeatedly dropped from different heights. The study revealed that the beam’s transient deflection was increased by about 50% with gre</p> ... Show More
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Publication Date
Sun Dec 02 2012
Journal Name
Baghdad Science Journal
Adsorption of Congo, Red Rhodamine B and Disperse Blue Dyes From Aqueous Solution onto Raw Flint Clay
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Removal of Congo red, Rhodamine B, and Dispers Blue dyes from water solution have been achieved using Flint Clay as an adsorbent. The adsorption was studied as a function of contact time, adsorbent dose, pH, and temperature under batch adsorption technique. The equilibrium data fit with Langmuir, Freundlich and Toth models of adsorption and the linear regression coefficient R2 was used to elucidate the best fitting isotherm model. Different thermodynamic parameters, namely Gibb’s free energy, enthalpy and entropy of the on-going adsorption process have also been evaluated. Batch technique has been employed for the kinetic measurements and the adsorption of the three dyes follows a second order rate kinetics. The kinetic investigations al

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Publication Date
Wed Jan 17 2018
Journal Name
Journal Of Engineering And Applied Sciences
PREPARATION, CHARACTERIZATION AND THERMAL ANALYSIS OF POLYMERIC BLEND NANOCOMPOSITES BASED ON PVA-PVPPEGDOPED WITH ZINC OXIDE NANOPARTICLES
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Publication Date
Thu Apr 21 2022
Journal Name
Journal Of Ecological Engineering
Simultaneous Adsorption of Ternary Antibiotics (Levofloxacin, Meropenem, and Tetracycline) by SunFlower Husk Coated with Copper Oxide Nanoparticles
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In this study, a new adsorbent derived from sunflower husk powder and coated in CuO nanoparticles (CSFH) was investigated to evaluate the simultaneous adsorption of Levofloxacin (LEV), Meropenem (MER), and Tetracycline (TEC) from an aqueous solution. Significant improvements in the adsorption capacity of the sunflower husk were identified after the powder particles had been coated in CuO nanoparticles. Kinetic data were correlated using a pseudo-second-order model, and was successful for the three antibiotics. Moreover, high compatibility was identified between the LEV, MER, and TEC, isotherm data, and the Langmuir model, which produced a better fit to suit the isotherm curves. In addition, the spontaneous and exothermic nature of the adso

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Publication Date
Tue Jan 01 2019
Journal Name
Current Research In Microbiology And Biotechnology
Detection of Anti-rubella virus, Cytomegalovirus and Chlamydia pneumonia antibodies in patients with type I diabetes mellitus
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Type-1 diabetes is defined as destruction of pancreatic beta cell, virus and bacteria are some environmental factor for this disease. The study included 25 patients with type-1 diabetes mellitus aged between 8 – 25 years from Baghdad hospital and 20 healthy persons as control group. Anti-rubella IgG and IgM, anti-Chlamydia pneumonia IgG and IgM were measured by ELISA technique while anti-CMV antibody were measured by immunofluorescence technique. The aim of current study was to know the trigger factor for type-1 diabetes. There were significant differences (P<0.05) between studied groups according to parameters and the results lead to suggest that Chlamydia pneumonia, CMV and rubella virus may trigger type-1 diabetes mellitus in Iraqi pat

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Complexes of Some Transition Metal with 2-Benzoyl thiobenzimidazole and 1,10-Phenanthroline and Studying their Antibacterial Activity
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Mixed ligands of 2-benzoyl Thiobenzimiazole (L1) with 1,10-phenanthroline (L2) complexes of Cr(III) , Ni(II) and Cu(II) ions were prepared. The ligand and the complexes were isolated and characterized in solid state by using FT-IR, UV-Vis spectroscopy, 1H, 13C-NMR, flame atomic absorption, elemental micro analysis C.H.N.S, magnetic susceptibility , melting points and conductivity measurements. 2-Benzoyl thiobenzimiazole behaves as bidenetate through oxygen atom of carbonyl group and nitrogen atom of imine group. From the analyses Octahedral geometry was suggested for all prepared complexes. A theoretical treatment of ligands and their metal complexes in gas phase were studied using HyperChem-8 program, moreover, ligands in gas phase

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Publication Date
Fri Jun 29 2012
Journal Name
Synthesis And Characterization Of Metal Complexes With Ligands Containing A Hetero (n) Atom And (hydroxyl Or Carboxyl) Group
Synthesis and Characterization of metal complexes with ligands containing ahetero (N) atom and (hydroxyl or carboxyl) group
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M(II) Ions using amino acid L- proline as a primary ligand and either Nicotinamide or 8- hydroxyqinoline as secondary ligand, respectively: a. The mixed ligand complexes of composition,[M(pro)2(na)2]. b. The mixed ligand complexes of composition , Na[M(pro)2(Q)]. Where proline (C5H9NO2) symbolized as pro H , Nicotinamide (C6H6N2O) symbolized as (NA) , 8- hydroxyqinoline, (C9H7NO2) symbolized as (8-HQ). The ligands and the metal chlorides were brought into reaction at room temperature (37ºc) in ethanol as solvent .The reaction required the following molar ratios [(1:2:2) metal:2NA:2pro-] and [(1:1:2) metal:Q:2pro-] with M+2 ions, where M = [Mn (II), Co(II), Ni(II), Cu(II), Zn(II), Cd(II) and pd(II)]. Products were found to be solid crystall

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Publication Date
Mon Apr 20 2020
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Nutritional Value of White Button Mushroom (Agaricus bisporus) Which is Most Widely Consumed in kurdistan regin-iraq
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This study was conducted in 2018, at Technical College of Applied Sciences, Sulaimani Polytechnic University, and Kurdistan Region-Iraq. The aim of the study was to determinate nutritional compositions and some elemental contents in marketable white button mushroom (Agaricus bisporus) that is collected in local markets of Kurdistan Region-Iraq. Five different samples (A: Penjwen product fresh, B: Sulaimani product fresh, C: American caned, D: Valencia Netherlandcaned and E: Erbil product fresh) were collected to be observed. The elements were analyzed by Atomic Absorption Spectrometry methods, and their chemical compassions were determined, too. The collected data were analyzed by One Way ANOVA. The highest fat, protein, fiber and dry matte

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