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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
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 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
Thu Apr 28 2022
Journal Name
Iraqi Journal Of Science
Synthesis, Characterization, and Biological Properties of Cr(III), Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) Complexes Derived from 1,3-Oxazol-5-(4H)-One
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New 1,3-oxazol-5(4H)-one(3) was synthesized by cyclization of[(4-Methyl phenyl-carbonyl)amino]acetic acid (2). The starting materials were readily obtained by acylation of 2-amino acetic acid (Glycine) with 4-methyl phenyl chloride .Imidazole(4) was synthesized by reaction of compound (3) with hydrazine hydrate (99%). Compound (4) was isolated and characterized by 1HNMR , FTIR , uv-vis spectroscopy and elemental analysis (C.H.N). Compound (4) has been used as a ligand (L) to prepare a number of metal complexes with Cr(III), Mn(II), Co(II), Ni(II) , Cu(II) and Zn(II).
The prepared complexes were isolated and characterized by FTIR and Uv-vis spectroscopy elemental analysis (C.H.N), flame atomic absorption technique, as well as magnetic

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Publication Date
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
Synthesis, Spectral and Dyeing Performance Studies of 4-(2-Aminmo-5-nitro-phenylazo)-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one Complexes with Some Metal Ions
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The ligand 4-(2-aminmo-5-nitro-phenylazo)-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one derived from 4-aminoantipyrine and 4-nitroaniline was synthesized. The synthesized ligand was characterized by 1HNMR, FT-IR, UV-Vis spectra and (C.H.N) analysis. Complexes of (YIII and LaIII ) with the ligand were prepared in aqueous ethanol with a 1:2 M:L ratio and at optimum pH. The prepared complexes were characterized by using flame atomic absorption, FT-IR, UV-Vis spectra,(C.H.N) analysis and conductivity measurement. The stoichiometry of complexes was studied by the mole ratio and job methods. A concentration range (1×10-4 - 3×10-4 M) obeyed Beer's law, the complex solutions show high values of molar absorption. On the basis of physicochemical

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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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Publication Date
Wed Mar 08 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Synthesis and Characterization of [Benzyl (2-hydroxy-1naphthylidene) hydrazine carbodithioate] and Its Metal Complexes With [Co(II), Ni(II), Cu(II), Zn(II), and Cd(II)] Ions
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  The formation of  Co(II), Ni(II), Cu(II), Zn(II), and Cd(II)-complexes (C1-C5) respectively was studied with new Schiff base ligand [benzyl(2-hydroxy-1-naphthalidene) hydrazine carbodithioate  derived from reaction of  2-hydroxy-1-naphthaldehyde and benzyl hydrazine carbodithioate. The suggested structures of the ligand and its complexes have been determined   by using C.H.N.S analyzer, thermal analysis, FT-IR, U.V-Visible, 1HNMR, 13CNMR , conductivity measurement , magnetic susceptibility and atomic absorption. According to these studies,  the ligand coordinates as  a tridentate with metal ions through nitrogen atom of azomethane , oxygen atom of  hydroxyl, and  sulfur atom of thione  

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Publication Date
Wed Jan 25 2012
Journal Name
Synthesis, Characterization And Antibacterial Activities Of Some Metal (ii) Heterocyclic Polyamine Complexes With 6,6'-(1,4-phenylenebis(azanediyl) Bis(2- Amino-6-methyl-6h-1,3-oxazin-4-ol) Ligand.
Synthesis, characterization and Antibacterial activities of some metal (II) heterocyclic polyamine complexes with 6,6'-(1,4-phenylenebis(azanediyl) bis(2-amino-6-methyl-6H-1,3-oxazin-4-ol) ligand.
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Publication Date
Thu Jan 01 2015
Journal Name
Chemistry And Materials Research
Synthesis, Physico-Chemical and Antimicrobial Activities Co(II),Ni (II) ,Cu(II), Zn(II),Cd(II) and Hg(II) Mixed- Ligand Complexes of L- Alanine and Trimethoprim Antibiotic
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The Co (II), Ni (II) ,Cu(II), Zn(II) ,Cd(II) and Hg(II) complexes of mixed of amino acid (L-Alanine ) and Trimethoprim antibiotic were synthesized. The complexes were characterized using melting point, conductivity measurement and determination the percentage of the metal in the complexes by flame (AAS). Magnetic susceptibility, Spectroscopic Method [FTIR and UV-Vis]. The general formula have been given for the prepared mixed ligand complexes [M(Ala)2(TMP)(H2O)] where L- alanine (abbreviated as (Ala ) = (C5H9NO2) deprotonated primary ligand, L- Alanine ion .= (C5H8NO2 -) Trimethoprim (abbreviated as (TMP ) = C10H11N3O3S M(II) = Co (II),Ni(II) ,Cu(II), Zn(II) ,Cd(II) and Hg(II). The results showed that the deprotonated L- Alanine by KOH (Ala

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Publication Date
Fri Dec 07 2018
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Effects of Aldosterone, Osteoprotegerin and Fibroblast Growth Factor-23 and Some Biochemical Markers in Chronic Kidney Disease Patients (Stage II-IV) among Patients with or without Cardiovascular Events
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Chronic Kidney Disease (CKD) is a public health problem and many studies support the link between kidney dysfunction and cardiovascular events.  Aldosterone has been shown for decades that a plasma aldosterone concentration is elevated in CKD. Whilst, Osteoprotegerin (OPG), after its capacity to protect bone, also osteoprotegerin is elevated in patients with chronic kidney disease (CKD), where it could predict the deterioration of kidney function, cardiovascular, vascular events and all-cause mortality. On the other hand, fibroblast growth factors (FGFs), in patients with CKD, its levels seem to increase progressively as kidney function worsens. The aim of the present study is to assess the correlations between serum osteoprotegerin

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Publication Date
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
Synthesis, Characterization, Antimicrobial and Theoretical Studies of V(IV),Fe(III),Co(II),Ni(II), Cu(II), and Zn(II)Complexes with Bidentate (NN) Donar Azo Dye Ligand
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The new 4-[(7-chloro-2,1,3-benzoxadiazole)azo]-4,5-diphenyl imidazole (L) have been synthesized and characterized by micro elemental and thermal analyses as well as 1H.NMR, FT-IR, and UV-Vis spectroscopic techniques. (L) acts as a ligand coordinating with some metal ionsV(IV), Fe(III), Co(II), Ni(II), Cu(II), and Zn(II). Structures of the new compounds were characterized by elemental and thermal analyses as well as FT-IR and UV-Vis Spectra. The magnetic properties and electrical conductivities of metal complexes were also determined. Study of the nature of the complexes formed in ethanol following the mole ratio method.. The work also include a theoretical treatment of the formed complexes in the gas phase, this was done using the (hyperch

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