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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 Jun 27 2021
Journal Name
Iraqi National Journal Of Nursing Specialties
Level of Depression and Anxiety among School Age Children with Acute Lymphoblastic Leukemia under Chemotherapy Treatment at Pediatric Teaching Hospitals in Baghdad City
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Objective(s): To assess the level of depression and anxiety among school age children with acute lymphoblastic leukemia under chemotherapy treatment and to find out the relationship between the level of depression and anxiety among the affected children and their demographic characteristics.
Methodology: A cross-sectional study was conducted on school age children both gender having acute lymphoblastic leukemia under chemotherapy treated and their age between 6 years to 12 years. The study started from the period of September, 19th 2020 to March,1st 2021. Non-probability (Purposive) sample of (114) children with acute lymphoblastic leukemia under chemotherapy was selected in attending hospital wards, outpatient and counseling clinics

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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
Tue Sep 01 2020
Journal Name
Meta Gene
Genetic polymorphisms frequency of vitamin D receptor gene rs7975232 and rs731236 in Iraqi thalassemic patients and healthy controls compared to Arabian healthy populations
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Publication Date
Thu Feb 16 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Qualitative and Quantitative Estimation or Chemical Constituents from Leaves and Roots of Iraqi Agave Attenuata by GC-MS and RP-HPLC(Conference Paper) #
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This research concentrate on cultivated Iraqi Agave attenuata dried leaves and roots, because of little studies on this plant especially on the root that lead to the eager of study and comparison of phytochemical constituents between leaves and root. Extraction of bioactive constituents was carried out using several solvents with increasing polarity (n-hexane, ethyl acetate and methanol) by soxhlet apparatus. Steroidal saponins in Agave genus is well documented in many species, lightening the minds in this research on extraction method which is specific for steroidal saponins. Phytochemical screening was done by GC/MS for n-hexane fraction, qualitative and quantitative estimation of several bioactive constituents (caffe

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Publication Date
Wed Aug 28 2019
Journal Name
International Journal Of Drug Delivery Technology
Synthesis, Characterization and Screening their Antibactrial Activity of some New Oxazepine and Diazepine Compounds Containing 1,3,4-Oxadiazole Ring Derived from L-Ascorbic Acid
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The search involve the synthesis of some new 1,3-oxazepine and 1,3-diazepine derivatives were synthesized from Schiff base. The Schiff base (VIII) prepared from reaction of aldehyde (IV) derived from L-ascorbic acid with aromatic amine ([2-(4- nitrophenyl)-5-(4-aminophenyl)-1,3,4-oxadiazole] (VII). Oxazepine compounds (IX-XI) were synthesized from the cyclic condensation of Schiff base (VIII) with (maleic, phthalic and 3-nitrophthalic) anhydride, compounds (IX-XI) that were reacted with p-methoxyaniline to give diazepine derivatives (XII-XIV). The structures of the new synthesized compounds have been confirmed by physical properties and spectroscopy measurements such as FTIR, and some of them by 1 H-NMR, 13 CNMR, Mass, and evaluated

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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
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
Fri Jan 24 2020
Journal Name
International Journal Of Pharmaceutical Research
Preparation, spectral characterization and biological activity of somenewbimetalic complexes derived from{ 2,2`((5-methyl-1,3-phenylene)-bis- (oxy))-bis-N`(E`)-2- hydroxybenzylideneacetohydrazide}ligand
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In this work, the preparation of new multidentate Schiff-base lig and and its metal complexes are described. The formation of the lig and{ 2,2`((5-methyl-1,3-phenylene)-bis-(oxy))-bis-N`(E`)-2- hydroxybenzylideneacetohydrazide}[H2L] was prepared from the reaction {2,2-((5-methyl-1,3-phenylene)-bis-(oxy))- di-(acetohydrazide)}[M]precursor and salicylaldehyde in a 1:2 mole ratio, respectively. The reaction of the lig and [H2L] with (Cr+3 , Mn+2 and Fe+2 )metal ions in a 1:2 (L:M) mole ratio. Ligand and complexes were characterised via spectroscopic analyses; [FT-IR, UV-Vis spectroscopy,(C.H.N) microanalysis, chloride content, thermal analysis(TG), electrospray mass, magnetic susceptibility and conductivity measurements. The characterisation d

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