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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
Sun Jun 01 2008
Journal Name
Baghdad Science Journal
Laboratory study on the effects of nutrient enrichment on a phytoplankton population in Sawa Lake, Iraq
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Nutrient enrichment of Sawa lake water was made using different nitrogen and phosphorus concentrations during autumn and spring at three stations. Different concentrations of nitrogen, phosphorus and N: P ratios were used to test variations in phytoplankton population dynamics. Nitrogen at a concentration of 25 µmole.l-1 and N: P ratio of 10:1 gave highest phytoplankton cell number at all stations and seasons. A total of 64 algal taxa dominated by Bacillariophyceae followed by Cyanophyceae and Chlorophyceae were identified. The values of Shannon index of diversity were more than one in the studied stations.

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Publication Date
Fri Jan 01 2021
Journal Name
Webology
The role of change management in achieving competetive advantage a case study in diyala state company
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The research aims to test the correlation relationships between wise leadership, and the business model, and to demonstrate its influence (wise leadership) on the business model. Therefore, two main hypotheses were put forward. The research was applied to a sample consisting of (87) managers and deputy managers, some of them are members on the board of directors of the researched company. The questionnaire was adopted as a basic tool for collecting data, in addition to personal interviews. A number of statistical methods were used to analyze the data and obtain results. The researcher showed a set of results, including: There is a significant correlation between wise leadership and business model. There is an influence of wise leadership on

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Engineering
A Prediction Formula for The Estimation of Sediment Load in The Upper Reach of Al-Gharraf River
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The presence of deposition in the river decreases the river flow capability's efficiency due to the absence of maintenance along the river. In This research, a new formula to evaluate the sediment capacity in the upstream part of Al-Gharraf River will be developed. The current study reach lies in Wasit province with a distance equal to 58 km. The selected reach of the river was divided into thirteen stations. At each station, the suspended load and the bedload were collected from the river during a sampling period extended from February 2019 till July 2019. The samples were examined in the laboratory with a different set of sample tests. The formula was developed using data of ten stations, and the other three s

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Publication Date
Tue Aug 26 2025
Journal Name
Al-kindy College Medical Journal
Metabolic Syndrome; Comparing the Results of Three Definition Criteria in an Iraqi Sample
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Background: Different diagnostic definition and criteria have been recommended by different expert groups for the diagnosis of metabolic syndrome, however, it’s prevalence in the same population could differ depending on the definition used yielding different results. In Iraq, there is a lack of research comparing these different diagnostic definitions.

Objective: To find out the most suitable metabolic syndrome definition to be used for Iraqi people.

 Methods: 320 participants were recruited for this study, 53.4% men and 46.6% women, aged between 25-85 years, visiting Baghdad Teaching Hospital, the prevalence of metabolic syndrome according to different definition

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Publication Date
Mon Jan 01 2018
Journal Name
Al-kindy College Medical Journal
Metabolic Syndrome; Comparing the Results of Three Definition Criteria in an Iraqi Sample
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Background: Different diagnostic definition and criteria have been recommended by different expert groups for the diagnosis of metabolic syndrome, however, it’s prevalence in the same population could differ depending on the definition used yielding different results. In Iraq, there is a lack of research comparing these different diagnostic definitions. Objective: To find out the most suitable metabolic syndrome definition to be used for Iraqi people.  Methods: 320 participants were recruited for this study, 53.4% men and 46.6% women, aged between 25-85 years, visiting Baghdad Teaching Hospital, the prevalence of metabolic syndrome according to different definitions were compared and the agreement was assessed by the Kappa st

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Publication Date
Fri Sep 04 2015
Journal Name
International Journal Of Academic Research In Progressive Education And Development
The Influence of Three Teaching Methods on Undergraduate Physics Students' Group Work Skill
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The purpose of this study is to compare the influence of three teaching methods, as represented by problem-based learning (PBL), the PBL with lecture method, and the conventional teaching on undergraduate physics students' group work skills among bachelor’s degree physics students. In this study, the pre- and post-test were done and the instruments were administered to the students for data collection. The actual sample size comprises of 122 students, who were selected randomly from the physics department, college of education in iraq. Overall, the statistical results rejected null hypothesis of this study. Thus, using the PBL without or with lecture method enhances the skills of the group work among the bachelor’s degree physics studen

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Publication Date
Mon Feb 01 2021
Journal Name
Iop Conference Series: Materials Science And Engineering
Performance Evaluation of a Combined Electrocoagulation– Electrooxidation Process for the Treatment of Petroleum Refinery Wastewater
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Abstract<p>The present study investigates the application of a combined electrocoagulation-electrooxidation (EC-EO) process for the treatment of wastewater generated from Al-Dewaniya petroleum refinery plant in Iraq. The EC-EO process was examined in terms of its ability to simultaneously produce coagulant and oxidant agents by using a parallel plate configuration system composed of stainless steel plates as cathode and pair of aluminum and graphite plates as anode at two different current concentrations (1.92A/l and 0.96A/l). The results showed that the best conditions for treatment of Al-Dewaniya petroleum refinery wastewater using the combined approach were current concentration of (0.96A/l), current density</p> ... Show More
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Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The effect of the marketing channel of the service on marine insurance losses: a case study in the Iraqi insurance company
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All businesses seek to improve their levels of profits through various means, most notably their marketing channels, which ensure the delivery of their products to their customers in a safe manner in a timely manner. It considers losses to a minimum and that insurance companies place great interest in marine insurance losses because they often constitute huge amounts compared to other losses, hence the problem of research, which is centred on the type and size of the impact owned by the channel The Iraqi insurance company was chosen to be applied according to the intentional sample method because this company is closely related to the subject matter. The research has reached a set of conclusions, most notably that the choice of i

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Publication Date
Wed Oct 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Spatial Regression Model Estimation for the poverty Rates In the districts of Iraq in 2012
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Theresearch took the spatial autoregressive model: SAR and spatial error model: SEM in an attempt to provide a practical evident that proves the importance of spatial analysis, with a particular focus on the importance of using regression models spatial andthat includes all of them spatial dependence, which we can test its presence or not by using Moran test. While ignoring this dependency may lead to the loss of important information about the phenomenon under research is reflected in the end on the strength of the statistical estimation power, as these models are the link between the usual regression models with time-series models. Spatial analysis had

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Publication Date
Tue Jan 01 2013
Journal Name
International Journal Of Contemporary Mathematical Sciences
Equivalent between the Criterion and the Three Open Set's Conditions in Disk-Cyclicity
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A vector in a separable infinite dimensional Hilbert space is called disk-cyclic for bounded operator if the orbit α : 0, α∈;|∝| 1is dense in. The useful tool used to discover codisk-cyclic operation is called the disk-cyclic Criterion. In this paper we will show that some equivalent conditions of the

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