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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
Sat Oct 01 2022
Journal Name
Journal Of Engineering
Parameters Affecting the Strength and Behavior of RC Dapped-End Beams: A Numerical Study
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The finite element method has been used in this paper to investigate the behavior of precast reinforced concrete dapped-ends beams (DEBs) numerically. A parametric investigation was performed on an experimental specimen tested by a previous researcher to show the effect of numerous parameters on the strength and behavior of RC dapped-end beams. Reinforcement details and steel arrangement, the influence of concrete compressive strength, the effect of inclined load, and the effect of support settlement on the strength of dapped-ends beams are examples of such parameters. The results revealed that the dapped-end reinforcement arrangement greatly affects the behavior of dapped end beam. The failure load decreases by 25% when

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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of Clinical And Experimental Dentistry
The effect of osseodensification on implant stability and bone density: A prospective observational study
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Background: The aims of this study were to evaluate the effect of implant site preparation in low-density bone using osseodensification method in terms of implant stability changes during the osseous healing period and peri-implant bone density using CBCT. Material and methods: This prospective observational clinical study included 24 patients who received 46 dental implants that were installed in low-density bone using the osseodensification method. CBCT was used to measure the bone density pre- and postoperatively and implant stability was measured using Periotest® immediately after implant insertion and then after 6 weeks and 12 weeks postoperatively. The data were analyzed using paired t-test and the probability value <0.05 was conside

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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
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
Thu Jun 01 2017
Journal Name
International Journal Of Science And Research
Precise Solutions of a Viscoelastic Fluid Flow in an Annular Pipe under an Impulsive Pressure with the Fractional Generalized Burgers' Model
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This paper deals with an analytical study of the flow of an incompressible generalized Burgers’ fluid (GBF) in an annular pipe. We discussed in this problem the flow induced by an impulsive pressure gradient and compare the results with flow due to a constant pressure gradient. Analytic solutions for velocity is earned by using discrete Laplace transform (DLT) of the sequential fractional derivatives (FD) and finite Hankel transform (FHT). The influences of different parameters are analyzed on a velocity distribution characteristics and a comparison between two cases is also presented, and discussed in details. Eventually, the figures are plotted to exhibit these effects.

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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
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
A study of anti fungal activity of a combination of essential oils from medical herbs against water molds
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The aim of this study is to evaluate the anti fungal activity of a combination of essential oils against water molds. HPLC analysis was done to evaluate the quantity and quality of the active compounds in this combination which extracted from three herbs( Peppermint Menthapiperita ,Thyme Thymusvulgaris, Common sage Salvia officinalis L.) and the active compounds are Camphor,Menthol,,Thujone and Thymol with different concentrations. In this study (MIC) , (MFC) were measured and (LD50) determined after 48,96 h from fingerlings treatment of common carp in aquariums .The results of (MIC) were 0.025µl/ml for Aphanomyces sp. and 0.015µl/ml for both Achlya sp. and Fusariumsolani which showed significant differences(p<0.05) from Malachite gre

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Publication Date
Thu Jun 30 2011
Journal Name
Al-khwarizmi Engineering Journal
Comparative Study of the Mechanical Properties of (FS) and MIG Welded Joint in (AA7020-T6) Aluminum Alloy
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A comprehensive practical study of typical mechanical properties of welded Aluminum alloy AA7020-T6 (Al-Mg-Zn), adopting friction stir welding (FSW) technique and conventional metal inert gas (MIG) technique, is well achieved in this work for real comparison purposes. The essences of present output findings were concentrated upon the FSW samples in respect to that MIG ones which can be summarized in the increase of the ultimate tensile strength for FSW was 340 MPa while it was 232 MPa for MIG welding, where it was for base metal 400 MPa. The minimum microhardness value for FSW was recorded at HAZ and it was 133 HV0.05 while it was 70 HV0.05 for MIG weld at the welding metal. The FSW produce 2470 N higher than MIG welding in the bending t

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Publication Date
Thu Apr 18 2019
Journal Name
Al-kindy College Medical Journal
Evaluation of Risk Management among Managers of the Primary Health Care Centers in Baghdad City: Comparative Study
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Background: Several risk managem-ent standards had been developed including the Project Management Institute, the National Institute of Standards and Technology, actuarial societies, and ISO standards.

Objective: The study aimed at evaluating risk management among managers of model and ordinary primary health care centers in Baghdad City and comparing the risk management among these centers.

Methods: A descriptive comparative des

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