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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 Feb 01 2024
Journal Name
Baghdad Science Journal
Traditional and molecular methods for diagnosing bacterial meningitis in Erbil city, Iraq
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Bacterial meningitis is a leading cause of illness and death worldwide. It is crucial for clinical and public health care, as well as disease control, to identify the meningitis-causing agent promptly. Between June 2021-February 2022, a total of 100 cerebrospinal fluid (CSF) and blood samples were collected from suspected cases of meningitis admitted to Raparin Paediatric Teaching Hospital, Erbil city-Iraq. Cytochemical, cultural, and biochemical tests were conducted, and confirmed by molecular techniques. Bacterial culture findings were positive in 7% of CSF samples and just one positive among blood samples. The most common pathogens found by cultural characteristics and VITEK 2 Compact System were Staphylococcus sciuri in two

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Publication Date
Mon Jan 01 2024
Journal Name
Computer Modeling In Engineering & Sciences
A Review and Bibliometric Analysis of the Current Studies for the 6G Networks
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Publication Date
Tue Mar 09 2021
Journal Name
Review Of International Geographical Education ( Rigeo )
Social Entrepreneurship and Women Empowerment in The Light of The Corona Pandemic": A Field Study from The Point of View of a Sample of Iraqi Women Entrepreneurs
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This research aims to clarify the conceptual framework of social entrepreneurship shows the importance of the development of social entrepreneurship according to the contextual aspects and the social value achieved from these works. It also identifies the degree of level of a sample of women entrepreneurs in Iraq for the extent of the relationship between social entrepreneurship and women's empowerment. It also explains the impact of entrepreneurial work in empowering women and the extent to which there are individual differences between the average scores of the sample members’ estimation of the level of social entrepreneurship according to social status, age group, educational qualification, and specialization according to the s

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Publication Date
Tue Jan 01 2019
Journal Name
Energy Procedia
The effect of the activation functions on the classification accuracy of satellite image by artificial neural network
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Publication Date
Wed Aug 13 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of sodium fluoride addition as a disinfectant on some properties of alginate impression material
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Background: Impression materials, impression trays, and poured stone cast have been said to be the main source of cross infection between patients and dentists. However, it was observed that disinfection of the impression is not performed systematically in routine dental practice. Disinfection of alginates either by immersion or spray technique was found to cause dimensional inaccuracies, although with proper disinfection of alginates there were small dimensional changes. A variety of fluoride releasing products designed for topical use is currently available. Following their use, varied amount of fluoride is systemically absorbed depending on the fluoride concentration and the manner of its use. The objective of this study was to evaluate

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Publication Date
Thu Jan 30 2014
Journal Name
Al-kindy College Medical Journal
Effects of Sleeve Gastrectomy as a Bariatric Surgery on Weight of Dietary Induced Obese Rats.
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Background: Obesity is becoming the healthcare epidemic world wide.Obesity is associated with reduced life expectancy, increased morbidity and mortality, and greater healthcare costs.Bariatric surgery is the only effective treatment for morbid obesity and is gaining increasing popularity. There has been a steady rise in the numbers and types of bariatric operations done worldwide in recent years butnon of prove to be ideal .Animal studies and use of animal models are significant element in the evolution of medical knowledge and the use of animals as a model for bariatric surgery is of importance to study the mechanisms of these operationsa and also help to develop new technique in management of obesity.Objectives:Study of effects of slee

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Publication Date
Tue Dec 30 2008
Journal Name
Al-kindy College Medical Journal
Use of Ascetic Fluid Cholesterol as a Marker to Differentiate between Types of Ascetic Fluid
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Background:- Cholesterol is high in ascetic fluid due
to malignancy and other causes of exudates.
Objective:-To use cholesterol as a marker to
differentiate between exudative and transudative
ascetic fluid and to compare that with other routine
parameters.
Methods:-Twenty eight patients were included in this
study 17 females with mean age of 41.9 years, 11
males with mean age of 48.2 years. The patients were
divided in group I suspected transudate, and group II
suspected exudate according to history and clinical
examination.
Ascetic fluid samples were sent for total protein,
albumin, and cholesterol measurement blood samples
were sent for serum protein and albumin measurement.
Results:-In this

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Publication Date
Sun Nov 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Assessment of some mechanical properties of PMMA/silica/zirconia nanocomposite as a denture base material
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Abstract<p>In this research, nanocomposites of poly(methyl methacrylate) (PMMA) and a mixture of nano silica (SiO<sub>2</sub>) and nano zirconia (ZrO<sub>2</sub>) were prepared in different weight percentages of the nano fillers to improve some of the properties of PMMA resin to be used as a denture base material. The nano filles were surface modified with a coupling agent and added to the PMMA in different amounts. Impact strength, transverse strength, hardness and roughness were tested for both control and experimental groups. The results indicate that PMMA/silica/zirconia nanocomposites, prepared with 5% by weight of both types of fillers, had a slight increase in impact s</p> ... Show More
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Publication Date
Wed Dec 12 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Study of Gender Differences in Health Promoting Behaviors for a Sample of Students Attending Institute of Technology, Baquba
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Objective: To find out any gender differences in health promoting behaviors for a sample of students attending Institute of Technology/ Baquba. Methodology: An analytical, cross-sectional study conducted randomly for a sample of students attending Technical Institute/ Baquba, during the period from 10th November 2015 to 10th April 2016. A questionnaire used to collecting data, this questionnaire was consisted from two domains related to health promoting behaviors including (Dietary domain and domain of some daily life activities like sleep duration, rise time, bedtime and walking period per week). The

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Publication Date
Wed Aug 13 2025
Journal Name
Journal Mustansiriyah Of Sports Science
The effect of using Daniel's model for people with two types of brain control (left and right) to learn the skill of the Cartwheel in artistic gymnastics for second-stage students
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The research problem focused through the researcher's experience in the gymnastics game and the lack of use of educational models that give the student an important role in the educational process, so it became necessary to identify the type of prevailing style for students, and the need for diversity in the use of educational models based on scientific theories, including the Daniel Document model. Based on three theories of learning, which are structural, behavioral, and meaningful learning. The research aimed to identify the effect of using the Daniel model for people with two types of brain control (left and right) to learn the skill of the Cartwheel in artistic gymnastics for students of the second stage. The researcher used the experi

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