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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 Oct 25 2017
Journal Name
Oriental Journal Of Chemistry
Synthesis and Antioxidant Ability of Some New 6-amino-7H- [1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-3-yl) Derivatives Bearing 2,6-Dimethoxy-4-(methoxymethyl)Phenol Moiety
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Publication Date
Sun Mar 01 2009
Journal Name
Baghdad Science Journal
Synthesis and Characterization of Tripodal Tetradentate Ligand Type NS3 and its Complexes with Re(V), Ni(II), Cu(II), Zn(II), Cd(II), and Hg(II)
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This work represents the preparation of the starting material, 3-chloro-2-oxo-1,4-dithiacyclohexane (S) using a new method. This material was reacted with, 4-phenylthiosemicarbazide to give (H3NS3) as a tetradentate ligand H3L. New complex of rhenium (V) with this ligand of the formula [ReO(L)] was prepared. New complexes of the general formula [M(HL)] of this ligand when reacted with some metal ions where: M = Ni(II), Cu(II), Cd(II), Zn(II), Hg(II) have been reported. The ligand and the complexes were characterized by infrared, ultraviolet–visible, mass, 1H nuclear magnetic resonance and atomic absorption spectroscopic techniques and by (HPLC), elemental analysis, and electrical conductivity. The proposed structure for H3L with Re (V) i

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Publication Date
Mon Mar 01 2010
Journal Name
Iraqi J Pharm Sci,
Synthesis, Characterization and Antibacterial Activities of Ligand Type N2O4 Schiff base and its Novel Complexes with Co(II), Ni(II), Cu(II) and Zn(II) ions
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The reaction of 2-amino benzoic acid with 1,2-dichloroethane under reflux in methanol and KOH as a base to gave the precursor [H4L]. The precursor under reflux and drops of CH3COOH which reacted with (2mole) from salicycaldehyde in methanol to gave a new type N2O4 ligand [H2L], this ligand was reacted with (MCl2) Where [M= Co (II), Ni(II), Cu(II) and Zn(II)] in (1:1) ratio at reflux in methanol using KOH as a base, to give complexes of the general formula [M(L)]. All compounds have been characterized by spectroscopic methods [1H NMR ( just to the ligand), FTIR, uv-vis, atomic absorption], melting point, conductivity, chloride content, as well as magnetic susceptibility measurements. From the above data, the proposed molecular structu

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Engineering
Passive Design Strategies to Enhance Natural Ventilation in Buildings "Election of Passive Design Strategies to Achieve Natural Ventilation in Iraqi Urban Environment with Hot Arid Climate"
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The natural ventilation in buildings is one of effective strategies for achieving energy efficiency in buildings by employing methods and ways of passive design, as well as its efficiency in providing high ranges of thermal comfort for occupants in buildings and raises their productivity. Because the concept of natural ventilation for many people confined to achieve through the windows and openings only, become necessary to provide this research to demonstrate the various passive design strategies for natural ventilation. Then, research problem: Insufficient knowledge about the importance and mechanism of the application of passive design strategies for natural ventilation in buildings. The research objective is: Analysis of passive desi

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Physics: Conference Series
Synthesis and Characterization of new Manganese(II), Cobalt(II), Cadmium(II) and Mercury(II) Complexes with ligand [N-(3-acetylphenylcarbamothioyl)-2-chloroacetamide] and their Antibacterial Studies
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Abstract<p>Addition chloro acetyl isothiocyanate (C<sub>3</sub>H<sub>2</sub>ClNOS) with 3-Aminoaceto phenone (C<sub>8</sub>H<sub>9</sub>NO) to prepare a fresh Ligand [N-(3-acetyl phenyl carbamothioyl)-2-chloroacetamide](L). The ligand (L) behaves as bidentate coordinating through O and S donor with metal ions, the general formula of all complexes [M(L)<sub>2</sub>(Cl)<sub>2</sub>](M<sup>+2</sup> = Manganese(II), Cobalt(II), Cadmium(II) and Mercury(II)). Compounds were investigation by Proton-1, Carbon -13 NMR spectra (ligand (L) only), Element Microanalysis for C, N, H, O, S, Fourier-transform infrared, UV visible, Conductance</p> ... Show More
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Publication Date
Thu May 05 2016
Journal Name
International Journal Of Science And Research (ijsr)
Mixed-1,10-phenanthroline with Mn(II), Cu(II),Co(II), Hg(II) and Ni(II) complexes Synthesis, Antimicrobial Activity and Spectroscopic Characterization of Binuclear Schiff Base
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The M(II) complexes [M2 (phen)2 (L)(H2O)2Cl2 ] in (2:1:2 (M:L:phen) molar ratio, (where M(II) =Mn(II), Co(II), Cu(II), Ni(II) and Hg(II), phen = 1,10-phenanthroline; L = 2,2'-(1Z,1'Z)-(biphenyl-4,4'-diylbis(azan-1-yl-1-ylidene))bis(methan-1-yl-1- ylidene)diphenol] were synthesized. The mixed complexes have been prepared and characterized using 1H and13C NMR, UV/Visible, FTIR spectra methods and elemental microanalysis, as well as magnetic susceptibility and conductivity measurements. The metal complexes were tested in vitro against three types of pathogenic bacteria microorganisms: Staphylococcus aurous, Escherichia coli, Bacillussubtilis and Pseudomonasaeroginosa to assess their antimicrobial properties. From this study shows that all the

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Publication Date
Tue Dec 01 2020
Journal Name
Egyptian Journal Of Chemistry
Synthesis, Characterization, Industrial And Biological Application Of Co(II),Ni(II),Cu(II) And Zn(II) Complexes With Azo Ligand Derived From Metoclopramide Hydrochloride And 3,5-Dimethylphenol
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Four complexes of Co(II),Ni(II),Cu(II) and Zn(II) with the azo ligand (4-chloro-N-(2-(dimethylamino)ethyl)-5-((2-hydroxy- 4,6-dimethylphenol)diazenyl)-2-methoxybenzamide) L. The structure of ligand and complexes were confirmed on the basis of their analytical and spectral data, these dyes were tested as dyeing in cotton fabric, and also testing in light and cleaner firmness. Also, antimicrobial and antifungal activities of ligand and their complexes were evaluated and the results showed that the ZnL compound showed the higher antibacterial activity with inhibition zone of 13mm against Staphyloco-ccus epidermidis, Steptococcus sp. and Escherichia coli compared with ligand and other metal complexes .In case of ZnL compound the antifungal acti

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Publication Date
Sun Jul 19 2020
Journal Name
Egyptian Journal Of Chemistry
Synthesis, characterization, industrial and biological application of Co(II),Ni(II),Cu(II) and Zn(II) complexes with azo ligand derived from metoclopramide hydrochloride and 3,5-dimethylphenol
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Four complexes of Co(II),Ni(II),Cu(II) and Zn(II) with the azo ligand (4-chloro-N-(2-(dimethylamino)ethyl)-5-((2-hydroxy-4,6-dimethylphenol)diazenyl)-2-methoxybenzamide) L. The structure of ligand and complexes were confirmed on the basis of their analytical and spectral data, these dyes were tested as dyeing in cotton fabric, and also testing in light and cleaner firmness. Also, antimicrobial and antifungal activities of ligand and their complexes were evaluated and the results showed that the ZnL compound showed the higher antibacterial activity with inhibition zone of 13mm against Staphyloco-ccus epidermidis, Steptococcus sp. and Escherichia coli compared with ligand and other metal complexes .In case of ZnL compound the antifungal activ

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of The College Of Languages (jcl)
Hidden messages in (Pour un oui ou pour un non) of Nathalie Sarraute: Les messages cachés dans "Pour un oui ou pour un non" de Nathalie Sarraute
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       The implicit is the narrative technique used to give indirect hidden messages. To read between the lines means to understand the implicit meaning that is not directly indicated. This technique is expressed in two forms: the hypothesis and the implications of linguistic and non-linguistic rules. Nathalie Sarraute’s "Pour un oui ou pour un non" states this narrative method through her character’s verbal and non-verbal dialogue. The present paper discusses the implicit method and shows the reason behind which  the author uses it in her play "Pour un oui ou pour un non".

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Publication Date
Sun Jun 02 2013
Journal Name
Baghdad Science Journal
Synthesis and Spectral Studies of Co(II),Ni(II),Zn(II) and Cd(II) Complexes with Ligand 2-[4- Carboxy methyl phenyl azo] -4,5-diphenyl imidazole (4CMeI)
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A new chelate complexes of Co(II),Ni(II),Zn(II) and Cd(II) were prepared by reacting these ions with the ligand 2-[4- Carboxy methyl phenyl azo]-4,5-diphenyl imidazole (4CMeI) The preparation were conducted after fixing the optimum conditions such as (pH) and concentration .UV- visible spectra of these complex solutions were studied for a range of (pH) and concentration which obey lampert-Beers Law.The structures of complexes were deduced according to mole ratio method which were obtained from the spectroscopic studies of the complex solutions .The ratios of metal: ligand obtained were (1:2) for all complexes..(UV-Vis) absorption spectra and The infrared spectra of the chelating complexes were studied ,this may indicate that coordination be

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