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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
Wed Jan 01 2020
Journal Name
Annals Of Tropical Medicine And Public Health
Phytochemical investigation And high performance thin layer chromatography (HPTLC) identification of flavonoids and phenolic acids in Euphorbia cyathophora (Family: Euphorbiaceae) cultivated in Iraq
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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
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
New Records of Non-Diatom Algae in Aquatic Habitat along Greater Zab River Path from Bekhma to Gwer District in Erbil Province, Iraq
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A study of non-diatom algal species composition in twelve sites from Greater Zab River path within
Erbil Province, was carried out from April 2021 to January 2022 with monthly sample collection in twelve studied sites. Among them site 4,5,6,7 and 9 are the first for algal study in this area. The 112 different species of algae belong to 33 genera, 25 families, 13 orders and 4 divisions have been identified. The predominant genera included Spirogyra and Cosmarium 17, 8 taxa respectively. 13 taxa were new recorded to Iraqi
Kurdistan algal flora and 9 of them were new recorded to Iraqi algal flora: Botryosphaerella sudetica, Muriella magna, Gloeotaenium loitlesbergianum, Apiocystis brauniana, Anabaena oscillarioides, C. distentum

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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 Jun 30 2016
Journal Name
Al-kindy College Medical Journal
Adenoidectomy with Myringotomy and Tympanostomy Tube Versus Adenoidectomy with Myringotomy in Treatment of Otitis Media with Effusion in 5-7 Years Old Children
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Background: Adenoiditis is a common cause of otitis media with effusion (OME) in children & perhaps OME is one of the most common diseases leads to hearing impairment in children with subsequent impairment of speech development & learning difficulties , however, treatment remains controversial. Objectives: To evaluate if there is a significant advantage of tympanostomy tube insertion in association with adenoidectomy over adenoidectomy in association with myringotomy alone in treatment of children with OMEType of the study: This is a prospective study. Patients & methods: The study consisted from 63 children diagnosed as cases of bilateral OME & variable degrees of adenoid hypertrophy. The patients were divided randomly i

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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
Sun Aug 06 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Complexeation Behavior of CoII, NiII, CuII, ZnII, and CdII Ions Toward Schiff Base Derived From 2, 4 -Dihydroxy Benzaldehyde and O-Phenylene Diamine
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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 (2,4dihydroxybenzylediene 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 comp

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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
Sun Sep 06 2015
Journal Name
Baghdad Science Journal
Microwave Assisted Synthesis, Solution State, Spectral Studies and Theoretical Treatment of Pd(II) , Pt(IV) and Au(III) ions Complexes Containing 2-Benzamide Benzothiazole
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2-benzamide benzothiazole complexes of Pd(II) , Pt(IV) and Au(III) ions were prepared by microwave assisted radiation. The ligand and the complexes were isolated and characterized in solid state by using FT-IR, UV-Vis spectroscopy, flame atomic absorption, elemental analysis CHNS , magnetic susceptibility measurements , melting points and conductivity measurements. The nature of complexes in liquid state was studied by following the molar ratio method which gave results approximately identical to those obtained from isolated solid state; also, stability constant of the prepared complexes were studied and found that they were stable in molar ratio 1:1.The complexes have a sequar planner geometry except Pt(IV) complex has octahedral .

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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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