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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 Mar 01 2021
Journal Name
Iraqi Journal Of Physics
Studying the Correlation Between Supermassive Black Holes and Star Formation Rate for Samples of Seyfert Galaxies (Type 1 and 2)
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An optical spectroscopic study is reported in this article to study the correlation between the supermassive black hole (SMBH) and the star formation rate (SFR) for a sample of Seyfert galaxies type (I and II). The study focused on 45 galaxy of Seyfert 1, in addition to 45 galaxy of Seyfert 2, where these samples have been selected form different survey of Salon Digital Sky Survey (SDSS). The redshift (z) of these objects were between (0.02 – 0.26). The results of Seyfert 1 galaxies shows that there good correlation between the SMBH and the SFR depending on statistical analysis parameter named Spearman’s Rank Correlation in a factor of (ρ=0.609), as well as the Seyfert 2 galaxies results show a good correlation between the SMBH

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Publication Date
Mon Mar 01 2021
Journal Name
Iraqi Journal Of Physics
Studying the Correlation Between Supermassive Black Holes and Star Formation Rate for Samples of Seyfert Galaxies (Type 1 and 2)
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An optical spectroscopic study is reported in this article to study the correlation between the supermassive black hole (SMBH) and the star formation rate (SFR) for a sample of Seyfert galaxies type (I and II). The study focused on 45 galaxy of Seyfert 1, in addition to 45 galaxy of Seyfert 2, where these samples have been selected form different survey of Salon Digital Sky Survey (SDSS). The redshift (z) of these objects were between (0.02 – 0.26). The results of Seyfert 1 galaxies shows that there good correlation between the SMBH and the SFR depending on statistical analysis parameter named Spearman’s Rank Correlation in a factor of (ρ=0.609), as well as the Seyfert 2 galaxies results show a good correlation between the SMBH and

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Publication Date
Fri Feb 13 2026
Journal Name
Journal Of Baghdad College Of Dentistry
The Effects of Different Investment Materials on Dimensional Accuracy and Surface Roughness of Thermosens Maxillary Complete Dentures
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Background: Limited data are available on the dimensional stability and surface roughness of ThermoSens, which is a material used in denture processing. This study aimed to measure the vertical teeth changes and surface roughness of ThermoSens dentures prepared using three different investment materials. Materials and methods: For the dimensional changes test, 30 complete maxillary dentures were prepared using different investment methods: group I, dental stone; group II, silicone putty; and group III, a mixture of dental stone and plaster (ratio, 1:1; n = 10 for each group). Four screws were attached to the dentures: two were attached to the buccal surface of the canine and first molar, and the other two were attached in the flange areas o

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Role of the evaluation process of the staff in determining the training programs Field research in the Office of the Inspector General of the Ministry of Health / Iraq
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         The objective of this research is to determine the relationship between the performance evaluation process and the training programs for the employees, to identify the extent of the organization's commitment to perform the performance evaluation process for its employees and to use the results of this process in determining the appropriate training programs. Performance evaluation, functional analysis, evaluation method used, dependent variable (training programs) and its dimensions, type of programs, program objectives, program curriculum, And the application of the field research methodology and the questionnaire, which included 146 individuals to know their views and analyz

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Publication Date
Mon May 01 2023
Journal Name
Rimak International Journal Of Humanities And Social Sciences
THE EFFECT OF ARRANGING WOMEN'S ISSUES IN THE IRAQI ELECTRONIC NEWSPAPERS' WEBSITES ON THE COGNITIVE LEVEL OF IRAQI UNIVERSITY FEMALE TEACHERS A FIELD STUDY OF A SAMPLE OF FEMALE TEACHERS AT THE UNIVERSITY OF BAGHDAD
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Women are considered the real power to build societies, as they are half of society, and it is their responsibility to raise generations، as human history testifies to the recording of great names with their giving and achievement in various scientific, social and humanitarian disciplines. Because of the importance of women in our lives, society must give them special care, whether at home or within the community structure to which they belong, so that they contribute to the image that brings about a transformation in the public scene, as well as providing them with support to take charge of bringing about change themselves, and this explains the interest of the press at all levels. Women's issues and topics through various journal

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Publication Date
Mon Jun 27 2022
Journal Name
. J Pharm Negative Results
Synthesis, Antioxidant, antibacterial and docking structure of new dihydro-pyrimidine derivatives containing multi phenol
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Newly series of 6,6’-((2-(Aryl)dihydropyrimidine-1,3(2H,4H)-diyl)bis(methylene))bis(2-methoxy phenol) (3a-i) were synthesized from cyclization of 6,6’-((propane-1,3-diylbis (azanediyl)) bis(methylene)) bis(2-methoxyphenol) with several aryl aldehyde in the presence of acetic acid. The newly compounds characterized from their IR, NMR and EIMs spectra. The antioxidant capacity of these compounds screened by utilizing DPPH and FRAP assays. Compounds 3g and 3i exhibited significant antioxidant capability in both assays. Docking study for these compounds as a potential inhibitors of gyrase enzyme were carried out. Compound 3g exhibited significant inhibition with binding free energies (DG) higher than novobiocin. compounds 2, 3a, 3b, 3

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Preparation of polymer thin film using as NH3 gas Sensor
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Polyaniline organic Semiconductor polymer thin films have been prepared by oxidative polymerization at room temperature, this polymer was deposited on glass substrate with thickness 900nm, FTIR spectra was tested , the structural,optical and electrical properties were studied through XRD ,UV-Vis ,IR measurements ,the results was appeared that polymer thin film sensing to NH3 gas.

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Publication Date
Mon Aug 01 2011
Journal Name
Journal Of Engineering
PROPERTIES OF HARDENED CONCRETE USING CRUSHED CLAY BRICK AS AGGREGATES
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This paper provides the result of an investigation to use of crushed clay brick as
aggregates in producing concrete. Eight different crushed clay brick aggregate concretes were
used in this investigation. Compressive strength, splitting tensile strength and pulse velocity of
crushed clay brick aggregates concrete were determined and compare to natural aggregate
concrete. The compressive strength of crushed clay brick aggregates concretes were always
lower than the compressive strength of natural aggregates concrete regardless the age of
concrete, but the crushed clay brick aggregates concrete showed better performance as the age of
concrete increases and average reduction in compressive strength were 33.5% at the age

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Publication Date
Thu Dec 01 2011
Journal Name
Journal Of Engineering
A GENERAL VELOCITY PROFILE FOR A LAMINAR BOUNDARY LAYER OVER FLAT PLATE WITH ZERO INCIDENCE
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A general velocity profile for a laminar flow over a flat plate with zero incidence is obtained by employing a new boundary condition to the other available boundary conditions. The general velocity profile is mathematically simple and nearest to the exact solution. Also other related values, boundary layer thickness, displacement thickness, momentum thickness and coefficient of friction are nearest to the exact solution compared with other corresponding values for other researchers.

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Publication Date
Wed May 11 2022
Journal Name
Journal Of Economics And Administrative Sciences
Comparing Some Methods For A single Imputed A missing Observation In Estimating Nonparametric Regression Function
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In this paper, we will study non parametric model when the response variable have missing data (non response) in observations it under missing mechanisms MCAR, then we suggest Kernel-Based Non-Parametric Single-Imputation instead of missing value and compare it with Nearest Neighbor Imputation by using the simulation about some difference models and with difference cases as the sample size, variance and rate of missing data.      

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