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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 May 01 2023
Journal Name
Environmental Nanotechnology, Monitoring & Management
Photodegradation of tetracycline antibiotic by ternary recyclable Z-scheme g-C3N4/Fe3O4/Bi2WO6/Bi2S3 photocatalyst with improved charge separation efficiency: Characterization and mechanism studies
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Publication Date
Sun Dec 27 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Isolation, Structural Characterization and Identification of Major Constituents in Ephedra foliata Naturally Growing in Iraq by TLC, GC-MS and UPLC-ESI-MS/MS
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Abstract:

   The aerial part of Ephedra foliata Family Ephedraceae have long been used in traditional medicine and now Ephedra species have medicinal, ecological, and commercial value. The variety of pharmacological actions of this plant is due to its chemical constituents. Ephedrine and
related alkaloids; are the newly potential medicinal value of Ephedra supplements for weight loss or performance improvement. Other pharmacological actions like antibacterial and antifungal effects of the phenolic acid compounds, the immunosuppressive action of the polysaccharides, and the antitumor action of flavonoids. The genus of this plant wildly distributed t

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Publication Date
Tue Oct 01 2024
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Assessment <b></b>of Serum P53 Protein Level in Adult Patients with Acute Myeloid Leukemia in Correlation with Response to Treatment
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Background: Acute myeloid leukemia (AML) is an adult leukemia characterized by rapid proliferation of undifferentiated myeloid precursors, leading to bone marrow (BM) failure and impaired erythropoiesis. The p53 tumor suppressor protein regulates cell division and inhibits tumor development by preventing cell proliferation of altered or damaged DNA. It orchestrates various cellular reactions, including cell cycle arrest, DNA repair, and antioxidant properties. Objectives: To investigate the relationship of P53 serum level with hematological findings, remission, and survival status in de novo AML patients. Methods: This is a cross-sectional study that enrolled 63 newly diagnosed de novo AML patients, and 15 sex- and age-matched healt

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Publication Date
Sun Sep 27 2020
Journal Name
Iraqi National Journal Of Nursing Specialties
Effectiveness of an Instructional Program Concerning Non-Pharmacological Guideline on Controlling Essential Hypertension among Patients at AL-Sader Hospital in AL-Najaf AL-Ashraf City
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Objective: The aims of present study to detect the effectiveness of instruction program of non-pharmacological guideline on blood pressure and laboratory test.

 

Methodology: A pre-experimental study was conducted in Al-Sader Teaching Hospital   from 8th of September 2019 to 25th of May 2020, in order to find out the effectiveness of instruction program concerning non-pharmacological guideline on controlling essential hypertension among patients. A non- probability (purposive sample) of 50 patients with essential hypertension is selected. Those patients are already diagnosed with Essential Hypertension

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Publication Date
Sat Sep 01 2012
Journal Name
Australian Journal Of Basic And Applied Sciences
Electrochemical interferences of Mn<sup>2+</sup> with Hg<sup>2+</sup>, Cd<sup>2+</sup> and Cu<sup>2+</sup> at different modified GCE
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Glassy carbon electrode (GCE) was modified with carbon nanotubes CNT and C60 by attachment and solution evaporation techniques, respectively. CNT/Li+/GCE and C60/Li+/GCE were prepared by modifying CNT/GCE and C60/GCE in Li+ solution via cyclic voltammetry (CV) potential cycling. The sensing characteristics of the modified film electrodes, demonstrated in this study for interference of Mn2+ in different heavy metals ion esp. Hg2+, Cd2+ and Cu2+. The interfering effect was investigated that exert positive interference on the redox peaks of Mn2+. The modification of GCE with nano materials and Li+ act an enhancement for the redox current peaks to observe the effect of interference for Mn2+ in 1:1 ratio with different heavy metals ion.

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Publication Date
Wed May 17 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Evaluation Interleukin ─ 8 and High Sensitivity C - Reactive Protein in Sera of Control Group and Human Female Patients with Osteoarthritis Nodal in Iraqi's Patients
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       The present study conducted on 30 female patients with osteoarthritis OA a attending Baghdad teaching hospital, in addition to 30 healthy females, all subjects were (35-65) year's old .Parameters were measured in the sera of patients group and healthy groups were interleukin -8 (IL-8) and high sensitivity C-reactive protein (hs-CRP).The results revealed a higher significant in all parameters of patients sera compared to healthy groups. Conclusion was obtained that IL-8 and hs- CRP were a markers or player inflammatory disease like osteoarthritis nodal  

 

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Publication Date
Sun Dec 06 2009
Journal Name
Baghdad Science Journal
Synthesis and Characterization of (Fe(II),Co(II),Ni(II) and Cu(II)) Complexes with Schiff Base derived from [benzoyl hydrazine] with [benzyl mono oxime]
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The reaction of [Benzoyl hydrazine] with [Diphenyl mono oxime] and Glacial acetic acid was carried out in methanol gave a new tridentate ligand [Benzoic acid (2-hydroxyimino- 1, 2-diphyneylethylidene) - hydrazide]. This ligand was reacted with some metal ions (Fe(II), Co(II), Ni(II), and Cu(II)) in methanol with (1:1) metal : ligand ratio to give a series of new complexes of the general formula [M(L)Cl2.H2O], where M= Fe(11), Co(11), Ni(11) and Cu(11). All compounds were characterized by spectroscopic methods (I.R, UV-Vis), elemental microanalysis (C.H.N), atomic absorption, magnetic susceptibility, and conductivity measurements. From the obtained data the proposed molecular structures were suggested for the complexes of Fe

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Publication Date
Fri Feb 28 2014
Journal Name
Journal Of Natural Sciences Research
Synthesis, Characterization and Antimicrobial Investigations of (Ag, Cu, Ni, Co, Mn and Hg) Complexes with Schiff Base Derived From PVA and Erythro-Ascorbic Acid Derivative
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The aim of this work is the synthesis of new Schiff base derived from PVA and Erythro-ascorbic acid derivative (pentulosono-ɣ-lactone-2,3-enedianisoate) and its metal complexes of biological significance. All synthesized compounds were characterized by Thin layer chromatography (TLC) and FTIR spectra and aldehyde was also characterized by (U.V-Vis), 1HNMR, 13CNMR and mass spectra. The synthesized Schiff base & its metal complexes were screened for their in vitro antimicrobial activity against five pathogenic bacteria (Escherichia coli, Shigella dysentery,Klebsiellapneumonae,Staphylococcusaureus, Staphylococcus Albus) and two fungal (Aspergillus Niger,Yeast).The biological activity ofall complexes is higher than free Schiff base ligand andf

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Publication Date
Sun Aug 13 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Synthesis and Characterization of Novel Ligand Type N2O2 and it,s Complexes With Cu(п) Co(п), Ni(п), Zn(п), and Cd(п) ions
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The reaction of ethylenediamine with [2,4,6-trihydroxyacetophenon] and KOH (Schiff Base) to gives the new tetradentate ligand 2-(1-{2-{1-2,6-Dihydroxy-4-methyl phenyl)ethyliden amino}- ethylimino}-ethyl-benzene- 1,2,5-triol [HCl]. This ligand was reacted with some metal ions (Cu(II), Co(II), Ni(II), Zn(II), and Cd(II)) in methanol with (1:1) metal :  ligand ratio to give a series of new complexes of the general formula [M(H4L)], where: M= Cu(11), Co(II), Ni(II), Zn(II), and Cd(II).      All compounds were characterized by spectroscopic methods [I.R, U.V.-Vis, C.H.N., analysis H.P.L.C, atomic absorption, magnetic susceptibility, (EI-mass for the ligand)], and microanalysis along with conductivity measurements

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Publication Date
Thu Dec 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Commercial banks in Iraq had applied in practice different forms of its activities upon surplus funds that deposited from individual, firms and many governments units
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These deposits take many forms like current acc, deposits in order to growth and serve national economy Various in varicose perspectives .

The problem of this paper its concern with un applied the mathematical models that used in profitability analysis of current acc , and deposits in view of risk, profit efficiency and financial leverage for this reason the paper discussion use the cumulate mathematical model to solve these problem, that content three variables that be used to measuring profitability by consequent replacement method by stable base and by moving base for 2007 – 2009 applied the data collect from Iraq middle east bank.           &nbs

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