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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 Sep 01 2019
Journal Name
Journal Of Global Pharma Technology
Synthesis and Characterization of Azo Dyes Ligands Complexes with Rh (III) and La (III) and Studies Their Industrial and Bacterial Application
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1-[4-(2-Hydroxy-4, 6-dimethyl-phenylazo)-phenol]-ethanone (HL1) and 2-(4-methoxy-phenylazo)-3, 5-dimethyl-phenol (HL2) were produced by combination the diazonium salts of amines with 3, 5-dimethylphenol. The geometry of azo compounds was resolved on the basis of (C.H.N) analyses, 1H and 13CNMR, FT-IR and UV-Vis spectroscopic mechanisms. Complexes of La (III) and Rh (III) have been performed and depicted. The formation of complexes has been identified by using elemental analysis, FT-IR and UV-Vis spectroscopic process as well, conductivity molar quantifications. Nature of complexes produced have been studied obeyed mole ratio and continuous alteration ways, Beer's law followed through a concentration scope (1×10-4 - 3×10-4 M). H

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Publication Date
Tue May 17 2022
Journal Name
Egyptian Journal Of Chemistry
Determination of Ferrous Ion in Pure & Pharmaceutical Preparation by Continuous Flow Injection Analysis Via Turbidmetric Utilizing NAG-4SX3-3D Analyzer
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Publication Date
Thu Dec 11 2025
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Circulating B-cell activating Factor in Multiple Myeloma Patients and Its Correlations with Serum Levels of β2-Microglobulin and Interleukin-6
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Background: Multiple myeloma (MM) is characterized by clonal proliferation of malignant plasma cells within the bone marrow. In most patients, monoclonal immunoglobulin heavy chains or light chains are produced and are associated with organ dysfunction. The growth factor B-cell activating factor (BAFF) plays an important role in the pathogenesis of multiple myeloma due to its ability to promote B-cell survival, expansion, and differentiation. Objective:  to measure the circulatory level of B-cell activating factor in multiple myeloma patients in relapsed and remission states and explore its possible correlations with the clinical staging, β2-microglobulin, and interleukin-6. Methods: This cross-sectional study was performed on 60

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Publication Date
Wed Oct 09 2019
Journal Name
Journal Of Global Pharma Technology
Synthesis, characterization, spectral of azo dyes ligands complexes with Rh(III) and La(III) and studies their industrial and bacterial application
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1-[4-(2-Hydroxy-4, 6-dimethyl-phenylazo)-phenol]-ethanone (HL1) and 2-(4-methoxy-phenylazo)-3, 5- dimethyl-phenol (HL2) were produced by combination the diazonium salts of amines with 3, 5- dimethylphenol. The geometry of azo compounds was resolved on the basis of (C.H.N) analyses, 1H and 13CNMR, FT-IR and UV-Vis spectroscopic mechanisms. Complexes of La (III) and Rh (III) have been performed and depicted. The formation of complexes has been identified by using elemental analysis, FTIR and UV-Vis spectroscopic process as well, conductivity molar quantifications. Nature of complexes produced have been studied obeyed mole ratio and continuous alteration ways, Beer's law followed through a concentration scope (1×10-4 - 3×10-4 M). High molar

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
Synthesis, Characterization and Biological Activity of Schiff Bases Chelates with Mn(II),Co(II),Ni (II),Cu(II) and Hg(II)
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In this paper, some series of new complexes of Mn(II), Co(II), Ni (II) Cu(II) and Hg(II) are prepared from the Schiff bases (L1,L2). (L1) derived from 4-aminoantipyrine and O-phenylene dia mine then (L2) derived from (L1) and 2-benzoyl benzoic acid. Structural features are obtained from their elemental microanalyses, molar conductance, IR, UV–Vis, 1H, 13CNMR spectra and magnetic susceptibility. The magnetic susceptibility and UV–Vis, IR spectral data of the ligand (L1) complexes get square–planar and tetrahedral geometries and the complexes oflig and (L2) get an octahedral geometry. Antimicrobial examinations show good results in the sharing complexes.

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
Synthesis, Characterization and Biological Activity of Schiff Bases Chelates with Mn(II),Co(II),Ni (II),Cu(II) and Hg(II)
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In this paper, some series of new complexes of Mn(II), Co(II), Ni (II) Cu(II) and Hg(II) are prepared from the Schiff bases (L1,L2). (L1) derived from 4-aminoantipyrine and O-phenylene dia mine then (L2) derived from (L1) and 2-benzoyl benzoic acid. Structural features are obtained from their elemental microanalyses, molar conductance, IR, UV–Vis, 1H, 13CNMR spectra and magnetic susceptibility. The magnetic susceptibility and UV–Vis, IR spectral data of the ligand (L1) complexes get square–planar and tetrahedral geometries and the complexes oflig and (L2) get an octahedral geometry. Antimicrobial examinations show good results in the sharing complexes.

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Publication Date
Sun Jul 05 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Periodontal health status in relation to physicochemical characteristics of saliva among pre-menopausal and post-menopausal women in Baghdad city-Iraq
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Background: Menopause can bring oral health problems and also associated with significant adverse changes in the orofacial complex. After menopause, women become more susceptible to periodontal disease due to deficiency of estrogen hormone. Current study aimed to evaluate the periodontal health status in relation to salivary constituent including pH, flow rate and some elements (Magnesium, Calcium and inorganic phosphorus) of pre and post-menopause women. Materials and Methods: Periodontal health status of 52 women aged 48-50 years old (26 pre-menopause and 26 post-menopause) were examined including (gingival index, plaque index, calculus index, probing pocket depth and clinical attachment level). Salivary sample was collected for two women

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Publication Date
Sun Jun 05 2022
Journal Name
Egyptian Journal Of Chemistry
Synthesis, Characterization, and Biological Activity of New Metal Ions Complexes with Schiff Base Derived from 2-Acetylthiophene and Isatin-3-Hydrazone
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This study describes the preparation of a new bidentate Schiff base derived from the condensation of Isatin-3-hydrazone with 2-acetylthiophene and the preparation of new series of complexes with a good yield. The prepared ligand was characterized by IR, UV-Vis, C.H.N.S elemental analysis, 1H and 13C NMR, LC-Mass spectroscopy, and physical measurements. Its complexes were analyzed by C.H.N.S elemental analyses, UV-Vis., FTIR, NMR, LC-Mass Spectra, atomic absorption spectroscopy, magnetic susceptibility, and conductivity measurements The results from spectroscopy and measurement studies showed that the ligand coordinated to the metal ion as a bidentate ligand via oxygen and nitrogen, forming an octahedral geometry around it. In vitro antimicr

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Publication Date
Mon Jun 01 2009
Journal Name
Al-khwarizmi Engineering Journal
Effect of Adding Alcohols and Gas Velocity on Gas Hold up and Mass Transfer Coefficient in Bubble Columns with Draught Tube
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     The bubble columns are widely used as a two or three phase reactor in industrial chemical process such as absorption, biochemical reactions, coal liquefaction, etc. To design such a column, two main parameters should be taken in consideration, the gas hold-up (), and the liquid phase mass transfer coefficient KLa. The study includes the effect of gas velocity and the addition of alcohols on gas hold-up and mass transfer coefficient in bubble column with draught tube when the length of the column is 1.5m and the ratio of the draught tube diameter to the column diameter equals 0.5 and the air dispersion into the base of the draught tube using a multi hole tuyere is equivalent to a diameter of 0.15 mm and

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Publication Date
Fri Nov 11 2011
Journal Name
Journal Of The European Optical Society: Rapid Publications
Transition from amplified spontaneous emission to laser action in disordered media of R6G dye and TiO2 nanoparticles doped with PMMA polymer
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