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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
Tue Feb 04 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
A Comparative Study on the Probability of Diabetes and Psychosocial Deficiency of Badminton Players Youth Category
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Many people believe that diabetes appears after a psychological crisis, which is a misconception but it could be in them before having a crisis ore the crisis. But emotion increases the appearance of symptoms, and athletes are at risk of developing diabetes. Hypoglycemia is not unusual for athletes, and during physical activity the sugar level changes in the blood. Therefore, it is important to conduct tests for the measurement of sugar before and immediately after the activity, for the purpose of detecting the sharp drop in the sugar level and treating it, and the early detection is necessary to avoid the possibility of diabetes, the concept of psychological immunity in psychology is considered a positive concepts that maintain the balance

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Publication Date
Thu Jun 04 2020
Journal Name
Fibers
A Comparative Study of the Performance of Slender Reinforced Concrete Columns with Different Cross-Sectional Shapes
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Most reinforced concrete (RC) structures are constructed with square/rectangular columns. The cross-section size of these types of columns is much larger than the thickness of their partitions. Therefore, parts of these columns are protruded out of the partitions. The emergence of columns edges out of the walls has some disadvantages. This limitation is difficult to be overcome with square or rectangular columns. To solve this problem, new types of RC columns called specially shaped reinforced concrete (SSRC) columns have been used as hidden columns. Besides, the use of SSRC columns provides many structural and architectural advantages as compared with rectangular columns. Therefore, this study was conducted to explain the structura

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Publication Date
Mon Mar 23 2020
Journal Name
Baghdad Science Journal
Surfactant Cloud Point Extraction as a Procedure of Preconcentrating for Metoclopramide Determination Using Spectro Analytical Technique
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In current article an easy and selective method is proposed for spectrophotometric estimation of metoclopramide (MCP) in pharmaceutical preparations using cloud point extraction (CPE) procedure. The method involved reaction between MCP with 1-Naphthol in alkali conditions using Triton X-114 to form a stable dark purple dye. The Beer’s law limit in the range 0.34-9 μg mL-1 of MCP with r =0.9959 (n=3) after optimization. The relative standard deviation (RSD) and percentage recoveries were 0.89 %, and (96.99–104.11%) respectively. As well, using surfactant cloud point extraction as a method to extract MCP was reinforced the extinction coefficient(ε) to 1.7333×105L/mol.cm in surfactant-rich phase. The small volume of organi

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of The College Of Education For Women
An Estimated Answer of a Condition between the Interpretive Structure and Surface Structure: Al-Qurtubi’s Tafseer as a Model: عمر عقلة خليف الدعجة
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This present work is concerned with one of the syntactic issues that has been researched by many linguists, grammarians, and specialists in Islamic studies, the estimated answer to a condition. However, this topic is researched this time by examining Imam Al-Qurtbi’s opinions in interpreting related ayas from the holly Quraan in his book (Collector of Quranic Rules) or its transliteration (Al-Jami’ Li Ahkam Al-Quran). Such a step involves commenting on, tracking what Al-Qurtbi said in this regard, discussing it from the points of view of other grammarians, and judging  it accordingly, taking into account the apparent surface structures of the examples collected. To achieve this objective, the inductive analytical approach has be

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Publication Date
Wed Jul 31 2019
Journal Name
Journal Of Engineering
Evaluation of the Accuracy of Digital Elevation Model Produced from Different Open Source Data
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This study aims to estimate the accuracy of digital elevation models (DEM) which are created with exploitation of open source Google Earth data and comparing with the widely available DEM datasets, Shuttle Radar Topography Mission (SRTM), version 3, and Advanced Spaceborne Thermal Emission and Reflection Radiometer Global Digital Elevation Model (ASTER GDEM), version 2. The GPS technique is used in this study to produce digital elevation raster with a high level of accuracy, as reference raster, compared to the DEM datasets. Baghdad University, Al Jadriya campus, is selected as a study area. Besides, 151 reference points were created within the study area to evaluate the results based on the values of RMS.Furthermore, th

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Publication Date
Thu Oct 23 2025
Journal Name
Baghdad Science Journal
Continuous Flow Injection-Turbidimetric Analysis for Determination of Cobalt (II) Ion in Alloys Using a Microcell with Irradiation Sources at 0–180° Using a Single Solar Cell as a Detector
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A cost-effective and efficient detector was created to conduct thorough turbidimetric measurements by reaction of Co (II) ion with calcium ferro cyanide to form bright green particulate, using the method of continuous flow injection analysis, the use of NAG-5SX1-1D-SSP Analyzer in determining cobalt (II) ion in a test for the validity of the new design. The NAG-5SX1-1D-SSP Analyzer is composed of five irradiation sources of white snow leds having the diameter of 10 mm with one solar cell of 55 mm length, 13.5 mm width. Using a selector switch to select the optimum voltage to be used which was 2.7 VDC. Under conditions of optimization, cobalt (II) ion was determined at 0.005–20 mmol. L–1(n = 23) while linearity dynamic range 0.005–7 mm

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Publication Date
Sun Mar 02 2008
Journal Name
Baghdad Science Journal
Determination Of Micro Amount Of Spironolactone In Some Of Pharmaceutical Preparate By Using a Molecular Luminescence Technique.
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The present study include a new developed method of analysis for determination of drug Spironolaction (SP) in some Pharmaceuticals by Spectrofluorometric method. Spironolaction was determined under optimal experimental condition that follows :- The excitation spectrum was (l=351 nm), the emmetion spectrum was (l=518 nm), pH=1, the suitable temperature for reaction 60oC and the optimal time less than (3) minute. The analysis and rang statistical data was:-Linear dynamic rang (1-10) ?g.ml-1, the detection limit (D.L = 0.023 ?g.ml-1), Molar absorptivity (? = 29875 liter mole-1 cm-1), Relative standard deviation (%RSD = 0.78), (%Erel = 3.3) and recovery (Rec = 96.6) percentage. Determination of Spironolactone was accomplished by two methods

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Publication Date
Mon Jun 28 2021
Journal Name
Journal Of The College Of Education For Women
The Developmental Role of Social Work in Reducing Social Extremism:A Field Study in Baghdad University-College of Mass Communication as a Model: محمد حميد علوان
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This study deals with the role that social work profession plays in all its fields to reduce social extremismat home, or school or within society. The study aims to: examine the historical roots of social work in the Iraqi society, investigate the objectives of the developmental role of social work, review the theories of social extremism, its characteristics, and causes, and to analyze the developmental role of social work to limit social extremism. To meet the objectives of the study, a descriptive analytical approach has been adopted. It involves using the social sampling survey method, i.e., a questionnaire tool in the University of Baghdad community-College of Media. The sample was randomly selected to include (100) students from th

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
A comparative study to determine the native eye lens protein in the some types of Iraqi vertebrates
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This study showed that the lens in baloot muluki fish Chondrostoma regium is transparent, spherical shape, and solid in textures, while in the tree frog Hyla arborea savignyi, freshwater turtles Clemmys caspia caspia, white–eared bulbul Pycnonotus leucotis and brown rat Rattus norvegicus are transparent, soft and biconvex, it is very soft in white–eared bulbul. There are many significant differences have been recorded between the average weight lens and the total concentration of the protein in the lens all studied animals. Electrical migration process for lens proteins showed that there is one bundle of crystalline –? and one bundle also crystalline–? in all studied species, either crystalline–? may represent one bundle character

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Publication Date
Sun Feb 15 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Tensile force measurement by using different lingual retainer wires, bonding materials types and thickness (A comparative in vitro study)
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Background: The bonded orthodontic retainer constructed from multistrand wire and composite is an efficient esthetic retainer, which can be maintained long-term. Clinical failures of bonded orthodontic retainers, most commonly at the wire/composite interface, have been reported. This in vitro investigation aimed to evaluate the tensile forces of selected multistrand wires and composite materials that are available for use in the construction of bonded fixed retainers. Materials and Methods: The study sample includes 120 wires with three types of retainer wires (3 braided strands\ Orthotechnology, 8 braided strands\ G&H Orthodontics, 6 coaxial strands\ Orthoclassic wires), two types of adhesive (flowable\ Orthotechnology, non flowable\ G&H O

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