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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 Dec 24 2018
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
MOLECULAR IDENTIFICATION AND PHYLOGENETIC-TREE ANALYSIS OF MONIEZIA SPECIES FROM SHEEP IN AL-DIWANIYAH CITY
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    The present study was performed to detect the molecular and the phylogenetic identification of species that belonging to the genus of Moniezia Blanchard, 1891 which affected intestines of sheep in Al-Diwaniyah city, Iraq; fifty intestine samples were sought for the infestation of Moniezia spp. from the city slaughterhouse from 1 October to 30 November 2017, this tapeworm was found to infest the intestines of 13 sheep.

 

    For morphological identify the genus of this tapeworm, eggs from one gravid proglottid of the thirteen worms were examined, polymerase chain reaction (PCR) and the PCR-product-based sequencing were applied on 4 Moniezia tapeworms targeti

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Publication Date
Sat Mar 01 2025
Journal Name
European Journal Of Ecology, Biology And Agriculture
Molecular Characterisation of Virulence Factors in Cryptococcus spp. Isolated from Humans, Pigeons, and Eucalyptus Sources
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This study aimed to isolate and identify Cryptococcus species from three distinct sources: sputum samples of pigeon fanciers, dried pigeon droppings, and eucalyptus tree leaves. A total of 150 specimens were collected over a two-month period, comprising 50 samples each from human sputum, pigeon droppings collected across various areas of Baghdad, and eucalyptus leaves obtained from the Baghdad College of Veterinary Medicine. All samples were cultured on Sabouraud dextrose agar supplemented with chloramphenicol and incubated at 25°C for 2–3 days. From the initial cultures, 20 isolates presumptively identified as Cryptococcus spp. were obtained: 6 isolates (12%) from human sputum, 9 isolates (18%) from pigeon droppings, and 5 isol

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Publication Date
Mon Jan 10 2022
Journal Name
Journal Of Biomimetics, Biomaterials And Biomedical Engineering
Synthesis, Molecular Modeling, DNA Damage Interaction, and Antioxidant Potential of Hesperidin Loaded on Gold Nanoparticles
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The flavonoglycone hesperidin is recognized as a potent anti-inflammatory, anticancer, and antioxidant agent. However, its poor bioavailability is a crucial bottleneck regarding its therapeutic activity. Gold nanoparticles are widely used in drug delivery because of its unique properties that differ from bulk metal. Hesperidin loaded gold nanoparticles were successfully prepared to enhance its stability and bioactive potential, as well as to minimize the problems associated with its absorption. The free radical scavenging activities of hesperidin, gold nanoparticles, and hesperidin loaded gold nanoparticles were compared with that of Vitamin C and subsequently evaluated in vitro using 2,2-diphenyl-1-picrylhydrazyl assay. The antioxi

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Publication Date
Sun Jul 01 2018
Journal Name
The Iraqi Postgraduate Medical Journal
Molecular and Serologic Detection of HLA-B27 among Ankylosing Spondylitis Patients with Some Clinical Correlations
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BACKGROUND: HLA-B27 can effect clinical presentation and course of ankylosing spondylitis. Different detection techniques of HLA-B27 are available with variable sensitivities and specificities. OBJECTIVE: To compare serologic and molecular diagnostic techniques of detecting HLA-B27 status and to correlate it with some clinical variables among ankylosing spondylitis patients. PATIENTS AND METHODS: A cross-sectional study was conducted on 83 Iraqi patients with ankylosing spondylitis. Clinical and laboratory evaluations were reported. HLA-B27 status was determined in all patients by real-time PCR using HLA-B27 RealFast™ kit; ELISA method was used as well to detect soluble serum HLA-B27 antigens using Human Leukocyte Antigen® kit. RESULTS:

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Publication Date
Sat May 02 2015
Journal Name
التربية العلمية
the effect of a strategy on the reading compreheehension of first-yearinter intermediate school students
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Publication Date
Sat Jul 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
A Statistical Analysis of the Effects of Afforestation on the Environment in Iraq (Northern Iraq)
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Abstract<p>The significance of the research conducted in northern Iraq comes despite the expansion of afforestation projects; yet, the suffering of the forests has increased due to their lack of scientific study, unpredictability of the climate, and adverse effects on the spread and growth of plant species Therefore, the goal of the study is to understand the effects of afforestation through a statistical analysis of plant diversity in northern Iraq and its distinctivenessThe analysis revealed that natural groupings had improved qualitatively more than other groups, particularly some dwindling species that are able to compete and occupy new areas. drought-prone vegetation, vegetation, and climat</p> ... Show More
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Publication Date
Sun Apr 03 2016
Journal Name
Journal Of Educational And Psychological Researches
The effect of a counseling program to develop the skills of friendship among introverts children
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Some children are suffering from introversion in kindergartens , so it must be confront and obviated by specialists because it will inevitably lead to unsatisfactory results reflect negatively on the individual and the community together . And the introvert child is a miserable child incapable of social interaction or give - and - take with colleagues , lack of integration of the child to life leads to the obstruction of  participation with his peers in various activities.     Introversion  causes a real emotional deficit to the children of kindergartens which limits of possibility of their intellectual development and mental growth and that because of their isolation and poor focus in education

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Publication Date
Thu Jul 01 2004
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
THE HAEMOPROTEIDS OF THE AVIAN FAMILY SCOLOPACIDAE IN IRAQ WITH DESCRIPTION OF A NEW SPECIES
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Three scolopacids out of 150 are found infected with Haemoproteus scolopaci Galli-
Valerio 1929 and H. tringae n. sp. A detailed description of the new taxon is presented along
with a comparison of the diagnostic measurements between the two species.

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Publication Date
Sun Apr 03 2011
Journal Name
Journal Of Educational And Psychological Researches
The use of the husband of violence against his wife who is a kindergarten teacher
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Wives generally and working wives especially may encounter in some
families forms of physical or psychological violence through all the
levels or whether it was a psychological intimidation or cursing and
insolence and detracting her human . value and the husband marries
another woman or uses physical abuse against her and beating and
sexual abuse of the wife are also included in this from . it is noticed that
the violent attitude of the husband may take one from or it may change
and alter with time for it might lead to the increase of the possibility of
violence to occur in different ways
The importance of this study comes out from the step that on which in
folds the problem of the use of the husband of vio

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Publication Date
Wed Sep 01 2021
Journal Name
Journal Of Applied Mathematics
The Dynamics of a Tritrophic Leslie-Gower Food-Web System with the Effect of Fear
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The avoidance strategy of prey to predation and the predation strategy for predators are important topics in evolutionary biology. Both prey and predators adjust their behaviors in order to obtain the maximal benefits and to raise their biomass for each. Therefore, this paper is aimed at studying the impact of prey’s fear and group defense against predation on the dynamics of the food-web model. Consequently, in this paper, a mathematical model that describes a tritrophic Leslie-Gower food-web system is formulated. Sokol-Howell type of function response is adapted to describe the predation process due to the prey’s group defensive capability. The effects of fear due to the predation process are considered in the first two levels

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