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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
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Groundwater Quality Study Based on the Existence of Escherichia coli as Bioindicator
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Abstract<p>The research aim was to observe the distribution pattern of <italic>Escherichia coli</italic> as groundwater pollution indicator in the most populous area, Matraman Sub-District Area in Jakarta, Indonesia (106°49’35” EL and 06°10’37” SL) consists of six (6) Urban Villages. The existence of <italic>Escherichia coli</italic> was measured with Most Probable Number (MPN) method as mentioned in Indonesian Standard Number 01-2332.1-2006. This research was also measure pollution parameter of Dissolved Oxygen (DO) and pH, and topography analyses used as well to determine groundwater flow direction. Groundwater sampling was conducted in several housings that have </p> ... Show More
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Publication Date
Mon Jan 01 2024
Journal Name
Baghdad Science Journal
Study of the Anticancer and Antimicrobial Biological Activity of a New Series of Thiohydantoin Derivatives
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        Recently, some prostate cancer patients have acquired resistance to the second -generation drugs (anzalutamide and apalutamide) prescribed for the treatment of this disease due to the emergence of the F876L mutation, which represents a challenge to modern medicine. In this study, a new series of 2-thiohydantoin derivatives were prepared through the reaction of different derivatives of maleimide (1c-4c) with isothiocyanate derivatives. The prepared compounds were diagnosed using FT-IR,1H-NMR ,13C-NMR, Mass spectra. The prepared series compounds has been studied against prostate cancer cells. The MTT assay was used to determine the activity of the prepared compounds against prostate cancer cells. The da

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Publication Date
Sun Mar 15 2020
Journal Name
Al-academy
Semiotic Transformations in Scenography of the Iraqi Theatre Show "The Play of Ali Al-Wardi and his Opponent- A Model": باسم محمد احمد حسن
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      Semiotics has been through wide experiences in various human sciences, especially in the fields of poetry, novel and myths. But its interest in the theatre and drama was much less and unique despite the richness of the theatrical connection as it is a probable field for the semiotic investigation which may require the semiotic approach in dealing with the theatrical and dramatic show during the two processes of: structural construction and deconstruction starting from a set of overlapping and interconnected texts inside the show, which can be limited in the text, then it would be difficult to semiotically cover all these complex and tricky texts. The theatre in its structural and aesthetic construction is c

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Publication Date
Thu Dec 25 2025
Journal Name
Retos
The effect of neurofeedback on free throw accuracy in female basketball players of Baghdad University
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Background: Female basketball players often face difficulties in maintaining free throw accuracy, particularly under psychological and neural pressure. Traditional training emphasizes physical skills, often neglecting cognitive and neurophysiological factors essential for precision performance. Objective: This study examined the effect of neurofeedback training on free throw accuracy in female basketball players at the University of Baghdad, comparing outcomes between an experimental group and a control group, and assessing associated neural changes. Methods: A quasi-experimental design involved two groups: an experimental group receiving neurofeedback to regulate brainwave activity, and a control group undergoing traditional traini

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Publication Date
Sun Mar 27 2022
Journal Name
Sport Tk-revista Euroamericana De Ciencias Del Deporte
Effect of resistance training on the biomechanics and accuracy of serve receiving skills in volleyball
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This study aimed to identify the effect of resistance training on the biomechanics and accuracy of serve receiving skills in volleyball. The research community was composed of 26 young volleyball players of Baghdad volleyball clubs. A total of 4 players were selected for the preliminary experiment, while 14 participants were recruited as the main sample for the study. In the present study, a set of resistance exercises were designed by the researchers for the volleyball players of the sample. Exercises were performed by the sample participants during the course of study. The biomechanical variables considered in the present study were: Preparation moment (shoulder joint angle, hip angle, knee joint angle), moment of pr

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Publication Date
Thu Nov 21 2024
Journal Name
F1000research
Comparison of the severity of urinary tract infections between Metformin and SGL2 Inhibitors among Iraqi Type 2 Diabetics.
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Background Many antidiabetic medications with distinct modes of action are available, The sodium glucose cotransporter-2 (SGLT-2) inhibitors are among the most recent oral antihyperglycemic medications. The American Diabetes Association recommends metformin, a biguanide medication, as the first option for oral control of type 2 diabetes because it has demonstrated promise in this regard. Aim of the study To evaluate and compare the effects of metformin and SGLT-2 inhibitors on general urine parameters in T2DM patients from Iraq. Method a prospective cohort study where 101 adult patients of both sexes aged under 70 years and newly diagnosed with T2DM, patients were divided into two groups, Metformin group (n=52), where metformin was p

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Publication Date
Tue Feb 05 2019
Journal Name
Journal Of The College Of Education For Women
Social Safety Nets and its role in the protection of widows (Problems and advancement options) A field study in the Social Welfare Department for Women
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Current search problem manifested and widows who community harsh to bear hardships and pains، The goals of continuing the sustainability of life and take responsibility, and especially in light of the difficult circumstances in which Iraq is going through, and the displacement of murder and terrorism, which generated huge numbers of widows and orphans Because of the loss of a breadwinner and which became women and children are the most harm to the victim and as a result of wars and armed tendencies So this research is an important and vital topic opens our horizons important for overlapping roles of women widows and their impact on the achievement and status of Iraqi women and that as long as aptly characterized and their ability to end

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Publication Date
Wed Mar 02 2022
Journal Name
Journal Of Educational And Psychological Researches
Student Attitudes towards Rooting the Educational Administration Field: A Field Study for Phd Students in the Department of Educational Administration at Umm al-Qura University
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The study sought to identify the attitudes of PhD students towards establishing the field of educational administration. The study followed the descriptive survey method. The questionnaire was used to collect information from the study community consisting of (95) male and female students in the department of educational administration and Planning. Among the most important results about students ’attitudes towards establishing the educational administration field are the following: 1) identifying the necessity of establishing the educational administration field. 2) Encouraging students to attend seminars and scientific conferences in Islamic rooting. 3) there are no statistically significant differences in the attitudes of doctoral s

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Publication Date
Tue Apr 14 2020
Journal Name
Modern Sport
The Effect of Using the Bybee Strategy(5ES) according to Brain Control Patterns in Learning a Kinetic Series on Floor exercises in Artistic Gymnastics for men
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The aim of this study to identify patterns of cerebral control (right and left) for second grade students in the collage of physical education and sports science of the University of Baghdad, as well as identify the definition of theThe Effect of Using the Bybee Strategy(5ES) according to Brain Control Patterns in Learning a Kinetic Series on Floor exercises in Artistic Gymnastics for menمجلة الرياضة المعاصرةالمجلد 19 العدد 1 عام 2020effect using the (Bybee) strategy (5ES) according to brain control patterns inlearning a Kinetic series on floor exercises In artistic gymnastics for men, andidentify the best combination between the four research groups learn, use Finderexperimental method research sample consi

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Publication Date
Mon Dec 16 2024
Journal Name
Light & Engineering
The Design and Experimental Realization of a Laser-Based Heating System Using Recycled Laser Module
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Laser is a powerful device that has a wide range of applications in fields ranging from materials science and manufacturing to medicine and fibre optic communications. One remarkable

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