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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 Dec 09 2018
Journal Name
Baghdad Science Journal
Application of Randomly Amplified Polymorphic DNA (RAPD) Technique to Estimate Genetic Distance among Some Methicillin Resistant Staphylococcus aureus Isolated from Different Iraqi Hospitals
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Methicillin resistant Staphylococcus aureus (MRSA) is one of the principal nosocomial causative agents. This bacterium has the capability to resist wide range of antibiotics and it is responsible for many diseases like skin, nose and wounds infection. In this study, randomly amplified polymorphic DNA (RAPD)-PCR was applied with ten random primers to examine the molecular diversity among methicillin resistant Staphylococcus aureus (MRSA) isolates in the hospitals and to investigate the genetic distance between them. 90 Isolates were collected from clinical specimens from Iraqi hospitals for a total of 90 isolates. Only 10 strains (11.11%) were found to be MRSA. From these 10 primers, only 9 gave clear amplification products. 91 fragment l

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Publication Date
Wed Aug 31 2022
Journal Name
Al-kindy College Medical Journal
Incorporation of Nurse Practitioners and Physician Assistants into patient care teams - Focus on infectious Diseases: Nurse practitioners and physician assistants in Infectious Diseases
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There is a global shortage of health care providers needed to address all levels of primary and specialty care.  The recent COVID-19 pandemic also highlights the importance and added value of health professionals with specialty training in infectious diseases.  In the United States, advanced practice providers (APPs) are being engaged to meet the expanding demand for generalist and specialist patient care.  The history and development of advanced practice registered nurses (APRNs) and physician assistants (PAs), are discussed as collaborative healthcare providers to promote better understanding of the ways they can be incorporated into a healthcare system.  An example of how APPs are utilized to provide both inpatient and outpatient

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Publication Date
Thu Jan 01 2009
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Complexeation Behavior of CoII, NiII, CuII, ZnII, and CdII Ions Toward Schiff Base Derived From 2, 4-Dihydroxy Benzaldehyde and O-Phenylene Diamin
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The aim of this work covers the synthesis and characterization of the new tertra dentate ligand (H4L) containing (N and O) as donor set atoms kind (N2O2) where: H4L=Bis-1,2 (2,4- dihydroxybenzylediene phylinediamine . The preparation of ligand contains reaction 2, 4 - Dihydroxy benzaldehyde and o-phenylene diamine . Schiff base was reacted with some metal ions in the presence of methanol to give the complexes in the general formula [M (H2L)] where: MII = Co, Ni, Cu, Zn, Cd. All compounds were characterized by spectroscopic methods I.R , U.V.-Vis, metal content and molar conductivity measurements, showed that the complexes are non-electrolyte. The proposed geometry for all of the proposed complexes was a tetrahedral while Ni complex was squa

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Publication Date
Wed Dec 12 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Relationship between Third Trimester Vaginal Bleeding Medical Causes and pregnancy Outcomes of Pregnant Women Attending Bint Al-Huda Hospital in Al-Nasiriya City
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Objective: To find out the relationship between vaginal bleeding during third trimester and pregnancy outcomes. Methodology: A purposive sample is "Non-probability" of (100) women who had diagnostic vaginal bleeding during third trimester (27-40wk) of pregnancy, and who visited the Bint Al-Huda Hospital for the period from 15th Feb. to 17th May 2015.Validity and reliability of questionnaire are determined through pilot study. Descriptive and inferential statistical procedures were used to analyze the data, and the data were collected by using interview technique, constructed questionnaire has been desig

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Publication Date
Wed Oct 08 2025
Journal Name
Key Engineering Materials
Improved Performance of Hydrogen Sulfide Gas Sensor Based on Zinc Oxide Nanostructures Thermally Synthesized Doped with Silver Nanoparticles and Multi-Walled Carbon Nanotubes
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The present work reports an approach of hydrothermal growth of ZnO nanorods, which simplifies the production of low cost films with controlled morphology for H2S gas sensor application. The prepared ZnO nanorods exhibit a hexagonal wurtzite phase analyzed by the X-ray diffraction analysis. The FTIR spectra provide information that the band located between 465-570 cm-1 corresponds to the stretching bond of Zn-O, which confirms the creation of ZnO. PL spectroscopic studies showed that the doping of Ag NPs and f-MWCNT in the ZnO matrix leads to the tuning of the bandgap. The SEM analysis showed the morphology of ZnO was the nanorods. The nanocomposites Ag/ZnO and F-MWCNT/ZnO which prepared, sep

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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
Sun Jan 01 2012
Journal Name
Natural Science
Determination of threshold random gain medium in dye: Polymer films containing TiO<sub>2</sub> nanoparticles
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Publication Date
Wed May 07 2008
Journal Name
Journal Of Kerbala University
Synthesis and Characterization of New Ligand type N2O2 and its complexes with (Co(II),Ni(II),Cu(II),Zn(II) and Cd(II) ions
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The [2-hydroxy -1,2-diphynel-ethanone oxime] was reacted with 1,2- dichloroethan to give the new ligand [H2L].this ligand was reacted with some metal ions (Co(II),Ni(II),Cu(II),Zn(II) and Cd(II) in methanol as a solvent to give a series of new (1:1)complexes of the general formula [ M(HL)]Cl ,( where : M= Co(II),Ni(II),Cu(II),Zn(II) and Cd(II)) are isolated All compounds have been characterized by spectroscopic methods [ I.R , U.V -Vis ] atomic absorption . Chloride content along with conductivity measurements. From the above data the proposed molecular structure for (Co, Cu, Ni, Zn and Cd) complexes adopting a tetrahedral structure.

Publication Date
Tue Jan 15 2008
Journal Name
Journal Of Kerbala University
Synthesis and Characterization of New Ligand type N2O2 and its complexes with (Co(II),Ni(II),Cu(II),Zn(II) and Cd(II) ions
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The [2-hydroxy-1, 2-diphynel-ethanone oxime] was reacted with 1, 2-dichloroethan to give the new ligand [H2L]. this ligand was reacted with some metal ions (Co (II), Ni (II), Cu (II), Zn (II) and Cd (II) in methanol as a solvent to give a series of new (1: 1) complexes of the general formula [M (HL)] Cl,(where: M= Co (II), Ni (II), Cu (II), Zn (II) and Cd (II)) are isolated All compounds have been characterized by spectroscopic methods [IR, UV-Vis] atomic absorption. Chloride content along with conductivity measurements. From the above data the proposed molecular structure for (Co, Cu, Ni, Zn and Cd) complexes adopting a tetrahedral structure

Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Pharmaceutical Sciences And Research
Synthesis of some Schiff base metal complexes involving trimethoprim and 2'-amino-4-chlorobenzophenone: Spectral, thermal, DNA Cleavage antimicrobial,antifungal and Cytotoxic activity studies
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In study of effective bioactive compounds, we have synthesized the Co((ІІ), Mn(ІІ), Fe(ІІ), Cu(ІІ), Ni(ІІ), and Zn(ІІ) complexes of the Schiff base derived from trimethoprim and2'-amino-4-chlorobenzophenone and characterized by spectroscopic (NMR, IR, Mass, UV–vis,), analytical, TGA studies and magnetic data .The solution electronic spectral study suggests the stoichiometry of the synthesized complexes and Elemental analysis detected the square planer and octahedral geometry of the compounds. The prepared metal complexes presented promoted efficiency versus the screened bacterial (Escherichia Coli and Staphylococcus aureus) antibacterial efficacy against (Staphylococcus aureus, Salmonella spp., E. coli, Vibrio spp., Pseud

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