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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 May 17 2021
Journal Name
Indian Journal Of Forensic Medicine & Toxicology
The Effect of Exercises with a Proposed Device to Improving Some Bio-Kinematic Variables and the Performance of the Arab Round off Skill on Floor Movement Mat Device of the Artistic Gymnastics for Women
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The importance of the research lies in preparing exercises using a proposed device to learn the skill of thehuman wheel on a machine rug of ground movements of the artistic gymnastics. As for the research problem:Through the presence of the two researchers as teachers and observers of this sport in the gymnastics hall,they noticed that there is difficulty in the students’ performance of the skill of the round off on the machineof the mat of ground movements, according to the researchers’ opinion, the reason for this is that skillsare taught with the limited availability of assistive devices, as well as the lack of use of these devices inexercises according to biomechanical variables, although they facilitate the learning process

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Publication Date
Tue Jul 14 2020
Journal Name
Baghdad Science Journal
The Green Synthesize of Zinc Oxide Catalyst Using Pomegranate Peels Extract for the Photocatalytic Degradation of Methylene Blue Dye
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In this study, the zinc oxide NPs have been synthesized from the fresh pomegranate peels extract using the precipitation method. The ZnO nanoparticles were produced from the reaction of fresh peels extract with zinc acetate salt which was used as zinc source in the presence of 2 M NaOH. The green synthesized nanoparticles were characterized through X-ray diffraction (XRD), UV-Vis diffuse reflection spectroscopy, Fourier transform infrared spectroscopy (FTIR), and Atomic force microscopy (AFM). The XRD patterns confirm the formation of hexagonal wurtzite phase structure for ZnO synthesized using pomegranate peels extract with average crystalline size of 28 nm. FTIR spectra identify the presence of many active functional groups for the pom

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Publication Date
Fri Apr 12 2019
Journal Name
Journal Of Economics And Administrative Sciences
The relationship between social capital and knowledge sharing and their impact on improving the educational service quality: an analytical study of the views of a sample of academic staffs in the government universities in the Kurdistan Region of Iraq
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Abstract

This study aims to find the relationships between social capital (social network, social trust, shared goals) and knowledge sharing (knowledge Donating, knowledge collecting) as independent variables and their impact on improving the quality of educational services (academic staffs quality, Quality of teaching methods and study curriculums). This research is an important, because it attempts to identify the relationship between social capital and the knowledge sharing and their effect on improving the quality of educational service for universities. The study problem was determined in several questions related to the nature of the correlation relationship - the impact between the different independent variables (

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Publication Date
Tue Jan 03 2023
Journal Name
College Of Islamic Sciences
Narrative Structures in the Novel “Qiamat Baghdad” for the Novelist Alia Talib – Semiotic Study
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Abstract

The human mind knew the philosophy and logic in the ancient times, and the history afterwards, while the semiotics concept appeared in the modern time, and became a new knowledge field like the other knowledge fields. It deals, in its different concepts and references, with the processes that lead to and reveals the meaning through what is hidden in addition to what is disclosed. It is the result of human activity in its pragmatic and cognitive dimensions together. The semiotic token concept became a knowledge key to access all the study, research, and  investigation fields, due to its ability of description, explanation, and dismantling. The paper is divided into two sections preceded by a the

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Publication Date
Tue Apr 01 2025
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Serological and Molecular Detection of Prevalence of Human Parvovirus (B19) in Beta Thalassemia Major Patients in Baghdad
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Background: Beta thalassemia major (β-TM) is an inheritable condition with many complications, especially in children. The blood-borne viral infection was proposed as a risk factor due to the recurrent blood transfusion regimen (hemotherapy) as human parvovirus B19 (B19V). Objective: This study investigated the B19V seroprevalence, DNA presence, B19V viral load, and B19V genotypes in β-TM patients and blood donors. Methods: This is a cross-sectional study incorporating 180 subjects, segregated into three distinct groups each of 60 patients, namely control, β-TM, and β-TM infected with Hepatitis C Virus (HCV).  For the B19V prevalence in the studied group, the ELISA technique and real-time PCR were used. The genotyping was follo

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Publication Date
Tue Jul 11 2023
Journal Name
Journal Of Educational And Psychological Researches
Content Assessment of the Sciences Textbooks of Grades (1-4) in the Light of International Standards in Mathematics and Science TIMSS 2019 (Cognitive Process Dimension)
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The current research aims to determine the requirements of Trends of International Mathematics and Science Study (TIMSS 2019) and to find out the extent to which the content of science textbooks for grades (1-4) in the Sultanate of Oman includes the requirements of (TIMSS 2019). Only the Cognitive Process dimension has been considered when conducting the analysis. The study population includes all science books from the first to the fourth grade for the academic year 2021-2022. The study identified and organized the requirements in the study tool, which is a list of requirements of (TIMSS 2019). After confirming its validity and reliability, the analysis was performed, and data were collected and analyzed statistically using frequencies

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Publication Date
Sun Sep 07 2025
Journal Name
Alqalam Journal Of Medical And Applied Sciences
Atypical Presentation of Fibroepithelioma of Pinkus: A Case Report and Review of the Literature
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Fibroepithelioma of Pinkus (FEP) is a slowly growing, low-grade malignant tumor with very low metastatic potential that is considered a distinct variant of basal cell carcinoma (BCC). It usually manifests as sessile or polypoidal lesions on the trunk of middle-aged patients. However, it may present in younger age groups, even in children. In this case, we present a rare case of FEP atypically presenting as a scaly plaque on the lower back for several years in an elderly female who was eventually diagnosed by excisional biopsy and histopathology.

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Publication Date
Sat Dec 31 2016
Journal Name
مجلة جامعة االنبار للعلوم البدنية والرياضية
The effects of Pilates exercises while using the ladder barrel device on fitness and coordinatedin performance for motor formations in artistic gymnastics for students
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The aim of the research was to prepare Pilates exercises using the barrel ladder apparatus and to identify the effect of Pilates exercises on agility, coordination, and motor sequences of third-year female students in artistic gymnastics. The researcher adopted the experimental method to achieve the objectives of the study and to verify its hypotheses, as it is suitable for the nature and problem of the research. In selecting the research population, the researcher carefully chose the sample using a purposive method, clarifying its elements and constituent units. The research population consisted of third-year female students at the College of Physical Education and Sports Sciences for Women / University of Baghdad, with a total of 20 stud

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Publication Date
Mon Jun 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
The possibility of Using the Low-Cost External Antenna with Smartphone for Accurate Surveying Applications by RTX Technology
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Abstract<p>Real Time Extended (RTX) technology works to take advantage of real-time data comes from the global network of tracking stations together with inventor locating and compression algorithms to calculate and relaying the orbit of satellite, satellite atomic clock, and any other systems corrections to the receivers, which lead to real-time correction with high accuracy. These corrections will be transferred to the receiver antenna by satellite (where coverage is available) and by IP (Internet Protocol) for the rest of world to provide the accurate location on the screen of smartphone or tablet by using specific software. The purpose of this study was to assess the accuracy of Global Navig</p> ... Show More
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Publication Date
Thu Sep 01 2016
Journal Name
Journal Of Engineering
Calculating the Transport Density Index from Some of the Productivity Indicators for Railway Lines by Using Neural Networks
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The efficiency evaluation of the railway lines performance is done through a set of indicators and criteria, the most important are transport density, the productivity of enrollee, passenger vehicle production, the productivity of freight wagon, and the productivity of locomotives. This study includes an attempt to calculate the most important of these indicators which transport density index from productivity during the four indicators, using artificial neural network technology. Two neural networks software are used in this study, (Simulnet) and (Neuframe), the results of second program has been adopted. Training results and test to the neural network data used in the study, which are obtained from the international in

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