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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 31 2023
Journal Name
Nativa,
Benthic invertebrate at three sites on the Tigris River, Iraq
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The study was conducted from November 2021 to May 2022 at the three study sites within the Baghdad governorate. The study aims to identify the impact of human activities on the Tigris River, so an area free of human activities was chosen and represented the first site. A total of 48 types were diagnosed, 6204 ind/m3 spread over three sites. The following environmental indicators were evaluated: Constancy Index (S), Relative abundance index (Ra), Richness Index (between 17.995 and 23.251), Shannon Weiner Index (0.48-1.25 bit/ind.), Uniformity Index (0.124 -0.323). The study showed that the highest percentage recorded was for the phylum Annileda 34%; and the stability index shows that taxes (Stylaria sp., Aoelosoma sp., Branchinra sowerby, Ch

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Scopus
Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Synthesis, Characterization and study biologicalactivity of several 1-cyclopentene-1,2-dicarboxylimidyl Containing oxadiazole and Benzothiazole
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In this work involved prepared of several new 1-cyclopentene-1,2-dicarboxylimide linked to oxadiazole and benzothiazole moiety were synthesized by two steps: The first step 2-amino-substituted-1,3,4-oxadiazoles and substituted-2-aminobenzothiazole were reaction with 1-cyclopentene-1,2-dicarboxyl anhydride producing N-( 5- substituted-1,3,4-oxadiazole-2-yl)-1-cyclopentene-1,2-dicarboxyl amic acids and N-(Substitutedbenzothiazole-2-yl)-1-cyclopentene-1,2-dicarboxyl amic acids which in turn were dehydrated in the second step via fusion method to afford he desirable N-(5-substituted-1,3,4-oxadiazole-2-yl)-1-cyclopentene-1,2-dicarboxylimides and N-(Substituted benzothiazole-2-yl)1-cyclopentene-1,2-dicarboxylimides respectively. Struct

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Publication Date
Wed Jun 03 2015
Journal Name
Al-ustath
Witchcraft and Women’s Spaces; A cultural Materialism Study of John Updike’s The Witches of Eastwick
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Witch stories are part of American popular culture, and this culture is extremely influenced by a continuing reliance on its past. The modern obsession of Americans with witches, whether real or metaphorical, is related to politics especially when it came to issues of gender politics. This article exposes a modern image of the female character seen from a male author point of view. John Updike, influenced by the changes that happened to women within second wave of feminism, attempted to write The Witches of Eastwick (1984). Actually, he presented women who did have a sort of careers. His witches are professional active and dynamic. What do witches stand for in American Culture? Why did Updike choose to write

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Water harvesting and sustainable spatial development A case study of the province of badra – zurbatiyah
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The major climate changes that have affected the planet in addition to wave the big drought plaguing the study area, including the lack of water for imports Badra River fatigue because of the Iran constructing dams on this river and make use of the waters for the benefitof its territory. The subject of finding sources of water has become available with the possibility of exploiting them in an exemplary manner is one of the key things in order to be exploited somewhere.
The study area was chosen within the eastern border of the province of Wasit within the district of Badra border, an area of (1557.5 km2) almost "to study the characteristics of hydrological and identify possibilities for water harvesting them. In this study was conduct

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Publication Date
Sat Jun 01 2024
Journal Name
Iraqi Journal Of Physics
A Study the Addition of Silver Dioxide on Some Optical Properties of Phosphate Bioactive Glass
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This study investigates the influence of silver oxide (Ag2O) concentration on the optical characteristics of phosphate bioactive glasses (PBGs). PBGs have emerged as promising alternatives to conventional silicate glasses in the medical field due to their excellent bioactivity and chemical resistance. Samples with varying Ag2O concentrations (0, 0.25, 0.5, and 0.75g) were sintered at 780°C for 2 hrs in an electric furnace. The samples were subjected to Fourier transfer infrared spectroscopy (FTIR), ultraviolet-visible (UV-Vis) spectroscopy, and photoluminescence (PL) tests to assess their functional groups and optical properties. By analyzing the FTIR spectrum of phosphate bioactive glass containing different amounts of Ag2O, it is

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Publication Date
Sun Mar 15 2020
Journal Name
Al-adab Journal
The Study and Analysis Grammatical of verbal sentence a fragment of "Zurita" (Leopoldo alas Clarín)
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This article deals with the study of theories about verbal periphrasis as a grammatical construction; the aim of this point it offers good and valid guidelines to improve the linguistic description. The interest in the subject comes from its importance in the process of language teaching for the students of Spanish and to clarify this type of curriculum of this research we analyzed a literary text. From "Zurita"

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Publication Date
Wed Feb 18 2026
Journal Name
Al-mustansiriyah Journal Of Science
Epidemiological Study to Investigate a Possible Vector of Visceral Leishmaniasisin the Central Region of Iraq
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An epidemiological study in Al-Mahmmodiya (50 km south Baghdad) to investigate a possible vector of Leishmaniasis were applied .This region is considered as a foci of Leishmaniasisaccording to the health association statistics. CDC light traps were used to collect the insects nightly. Insects were collected by Indoor application as human dwellings and animal shelters and Outdoor application as rodent's barrows and field trees. Sand flies were transported to the laboratory, isolated and identified according to the identification keys in Tropical Biological Researches Unit at the Collage of Science / University of Baghdad. Must of the collected sand flies were belonging to three species PhlebotomuspapatasiScopoli(45%), PhlebotomusalexandriSin

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Crisis management effective of business organizations in the era of managerial technique: a philosophical study
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At a time of increasing human potential in the face of crises and risks through the use of technology on a large scale and steadily in various fields of life, and the vulnerability of business organizations as a result of mistakes. The failure of a sudden these errors or omissions or symptoms. Also, some crises occur outside the control of management, others caused by leakage of important information and sometimes secret may be a strategy or a new plan or new project occurs outside the organization to the opposite of what is planned. Therefore, the crisis management are critical to all organizations, because the active management of the crisis helps to ensure the continued prosperity of the organization. Here comes from the resea

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Publication Date
Sat Apr 01 2023
Journal Name
Egyptian Journal Of Veterinary Sciences
Effect of Crocin on the Spermatogenesis Indices of Mice Testis: A Histopathological and Histomorphological Study
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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Engineering
Chemical-Free Greywater Treatment Using Aeration, Sedimentation, Followed by Granular Activated Carbon Filter (GAC) -A Case Study of Baghdad city household
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Greywater is a possible water source that can be improved for meeting the quality required for irrigation. Treatment of greywater can range from uncomplicated coarse filtration to advanced biological treatment. This article presents a simple design of a small scale greywater treatment plant, which is a series of physical and natural processes including screening, aeration, sedimentation, and filtration using granular activated carbon filter and differentiates its performance with sand filter. The performance of these units with the dual filter media of (activated carbon with sand) in treatment of greywater from Iraqi house in Baghdad city during 2019 and that collected from several points including washbasins, kitchen si

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