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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
Sun Mar 04 2012
Journal Name
Baghdad Science Journal
Evaluation of cellular immune response in Golden Hamsters experimentally infected with Leishmania donovani comparing with cellular immune response against chicken Red Blood Cells.
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The Evaluation of the immune response in Golden Hamsters experimentally infected with Leishmania donovani was determined in this study, particularly, the cellular immune response. Follow up has maintained to determine the Delayed Type of Hypersensitivity using skin test both in infected and control lab animals. Chicken red blood cells were used as a parameter to evaluate the immune system; they are dull and have the ability of immunization. Two concentrations of chicken R.B.C were examined to determine which gives the higher titration in Hamsters and those were 1.5 X 109 cell/ml and 3 X 109 cell/ml , the second concentration gave the maximum titration where then used in this work. After sensitization with Chicken R.B.C for both infected a

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Publication Date
Tue Mar 19 2024
Journal Name
Baghdad Science Journal
Synthesis, Spectroscopic, and Characterization of Novel Nano Sized Mannich Base Complexes with Pt (IV) and Au (III) Ions and Assessing Their Antioxidants Activity
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في هذا البحث تم تحضير المركبات المعدنية النانوية الجديدة لأيونات البلاتين 4+و الذهب 3+ مع ليكاند قاعدة مانخ جديد مشتق من السيبروفلوكساسين بطريقة الموجات فوق الصوتية. تم تشخيص المعقدات النانوية والليكاند الجديد بأستخدام  تقنيات فيزيائية و كيميائية مختلفة مثل أطياف الاشعة تحت الحمراء، حيود الاشعة السينية ، المجهر الالكتروني الماسح ، المجهر الالكتروني النافذ و مجهر القوة الذرية.  تم تحديد نشاط مضادات الأك

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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
Thu Mar 09 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
New Schiff Base Derived From Folic Acid and 3Aminoacetophenone and its Metal Complexes with Some Transition Metals and Evaluation of Their Biological Activity
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The ligand [Potassium (E)-(4-(((2-((1-(3-aminophenyl) ethylidene) amino)-4-oxo-1, 4-dihydropteridin-6-yl) methyl) amino) benzoyl)-L-glutamate] was prepared from the condensation reaction of folic acid with (3-aminoacetophenone) through Schiff reaction to give a new Schiff base ligand [H2L]. The ligand [H2L] was characterized by elemental analysis CHN, atomic absorption (AA),(FT-IR),(UV-Vis), TLC, ES mass (for spectroscopes), molar conductance, and melting point. The new Schiff base ligand [H2L], reacts with Mn (II), Co (II), Ni (II), Cu (II), Cr (III) and Cd (II) metal ions and (2-aminophenol),(metal: derivative ligand: 2-aminophenol) to give a series of new mixed complexes in the general formula:-K3 [M2 (HL)(HA) 2],(where M= Mn (II) and Cd

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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
Thu Aug 01 2013
Journal Name
Desalination And Water Treatment
Competitive biosorption of Pb(II), Cr(III), and Cd (II) from synthetic wastewater onto heterogeneous anaerobic biomass in single, binary, and ternary batch systems
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Biosorption of lead, chromium, and cadmium ions from aqueous solution by dead anaerobic biomass (DAB) was studied in single, binary, and ternary systems with initial concentration of 50 mg/l. The metal-DAB affinity was the same for all systems. The main biosorption mechanisms were complexation and physical adsorption of metallic cations onto natural active functional groups on the cell wall matrix of the DAB. It was found that biosorption of the metallic cations onto DAB cell wall component was a surface process. The main functional groups involved in the metallic cation biosorption were apparently carboxyl, amino, hydroxyle, sulfhydryl, and sulfonate. These groups were part of the DAB cell wall structural polymers. Hydroxyle groups (–O

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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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Publication Date
Wed Jun 10 2015
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
New Schiff Base Derived From Folic Acid and 3- Aminoacetophenone and its Metal Complexes with Some Transition Metals and Evaluation of Their Biological Activity
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The ligand [Potassium (E)-(4-(((2-((1-(3-aminophenyl) ethylidene) amino)-4-oxo-1,4- dihydropteridin-6-yl) methyl) amino)benzoyl)-L-glutamate] was prepared from the condensation reaction of folic acid with (3-aminoacetophenone) through Schiff reaction to give a new Schiff base ligand [H2L]. The ligand [H2L] was characterized by elemental analysis CHN, atomic absorption (A.A), (FT-I.R.), (U.V.-Vis), TLC, E.S. mass (for spectroscopes), molar conductance, and melting point. The new Schiff base ligand [H2L], reacts with Mn(II), Co(II), Ni(II), Cu(II), Cr(III) and Cd(II) metal ions and (2-aminophenol), (metal : derivative ligand : 2-aminophenol) to give a series of new mixed complexes in the general formula:- K3[M2(HL)(HA)2], (where M=Mn(II) and

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Publication Date
Wed Jun 11 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Cone Beam Computed Tomography in an Evaluation and Diagnosis of Anatomical Variations and Pathological Lesions in Maxillary Sinus Prior to Maxillary Sinus Lift Surgery
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Abstract: Thorough assessment of the Maxillary,Sinus is very important. Recently 3-dimensional imagewith Cone Beam Computed Tomography (CBCT) is very dependable in Maxillary Sinus diagnosis. The aim of this study is to: shade light on the role of (CBCT) diagnosis of the maxillary sinus anatomical variation and pathological finding among smokers and nonsmokers prior to maxillary sinus lift techniques. Materials and Method: In this study 60 males with age ranged between 20-50 years old, referred for (CBCT) assessment of maxillary sinus in the Specialist Health Center of AL-Sadder city. The scanning were performed using Kodak 9500 (CBCT), the KV was 90, mA10 and scanning time 10 s. Voxel size 0.3mm with( DICOM ) software on a multiplaner re

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