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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
Sat Apr 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The Effect of Strategic Intelligence in High performance organization A Survey Study for the Managers of Diseases and Kidney Transplant Center/ Medicine City-Baghdad
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The topic of strategic intelligence is considered as important topics that acquires the attention of organizations, Because of its role in supplying the decision-making centers by strategic ideas according to the opportunities and threats facing the organization, in an effort to improve the performance of their organizations to reach the high performance organization.

A lot of organizations lack to strategy guides the strategic intelligence towards achieving high performance organization.

This research aims to determine the level of strategic intelligence that characterized the leaders of diseases and kidney transplant center in Medicine city. What is the application level of the

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Publication Date
Fri Apr 12 2019
Journal Name
Journal Of Economics And Administrative Sciences
Balanced Scorecard (BSC) role And Six Sigma in improving strategic performance A sample study of the members of the General Company for Northern Cement
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Assessing performance efficiency is critical to the management need for oversight, planning, and continuous periodic evaluation of the multiple activities of Northern Cement State Company in order to determine the level of achievement of the objectives set, and to correct the deviations and delays that the evaluation shows and limitation of liability. What cannot be measured cannot be managed. The aim of this research is to highlight the impact of using BSC, financial and non-financial, to give comprehensive and clear picture of the company's performance and to measure the quality of its performance by using six-sigma and the level of deviations in achieving the planned goals. Therefore, four-key hypotheses were formulated for th

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Publication Date
Wed Sep 11 2024
Journal Name
Edelweiss Applied Science And Technology
The effectiveness of a proposed strategy according to the Fraunhofer model of knowledge management in the achievement of second intermediate female students in mathematics
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The goal of the research is to identify the effectiveness of using a proposed strategy according to the Fraunhofer model of knowledge management in mathematics achievement for second-grade female students in middle and high schools affiliated with the General Directorate of Education in Baghdad / Al-Karkh II. The objective was to prove the following null hypothesis: "The average scores of the experimental group who will study with the proposed strategy according to the Fraunhofer model and the scores of the control group students who will study in the usual way in the mathematics achievement test are not statistically significant different at the significance level (0.05)." The General Directorate of Education of Baghdad / Al-Karkh

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Publication Date
Mon Feb 01 2016
Journal Name
Journal Of Engineering
Deterioration Model for Sewer Network Asset Management in Baghdad City (case study Zeppelin line)
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Asset management involves efficient planning of economic and technical performance characteristics of infrastructure systems. Managing a sewer network requires various types of activities so the network can be able to achieve a certain level of performance. During the lifetime of the network various components will start to deteriorate leading to bad performance and can damage the infrastructure. The main objective of this research is to develop deterioration models to provide an assessment tool for determining the serviceability of the sewer networks in Baghdad city the Zeppelin line was selected as a case study, as well as to give top management authorities the appropriate decision making. Different modeling techniques

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Publication Date
Tue Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
Designing a Quality System using the Goals Programming Method -An Applied Research
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Due to the continuous development in society and the multiplicity of customers' desires and their keeping pace with this development and their search for the quality and durability of the commodity that provides them with the best performance and that meets their needs and desires, all this has led to the consideration of quality as one of the competitive advantages that many industrial companies compete for and which are of interest to customers and are looking for. The research problem showed that the Diyala State Company for Electrical Industries relies on some simple methods and personal experience to monitor the quality of products and does not adopt scientific methods and modern programs. The aim of this research is to desi

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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 Jul 10 2023
Journal Name
Journal Of Engineering
Bearing Capacity of a Strip Model Footing on Loose Sand Reinforced With Pomegranate Sticks Mat
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A series of laboratory model tests has been carried out to investigate the using of pomegranate sticks mat as reinforcement to increase the bearing capacity of footing on loose sand. The influence of depth and length of pomegranate sticks layer was examined. In the present research single layer of pomegranate sticks reinforcement was used to strengthen the loose sand stratum beneath the strip footing. The dimensions of the used foundation were 4*20 cm. The reinforcement layer has been embedded at depth 2, 4 and 8 cm under surcharge stresses . Reinforcing layer with length of 8 and 16 cm were used. The final model test results indicated that the inclusion of pomegranate sticks reinforcement is very effective in improvement the loading cap

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Publication Date
Mon Jan 01 2018
Journal Name
Portugaliae Electrochimica Acta
A Kinetic Study of Oxalic Acid Electrochemical Oxidation on a Manganese Dioxide Rotating Cylinder Anode
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Publication Date
Sat Apr 01 2017
Journal Name
Al–bahith Al–a'alami
Digital Communication: The Future of Identity in Arab TV Drama: A Field Study on a Sample of Arab Society in the UAE in 2017
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The digital communication of a product of communication and information revolution. It is characterized by accurate and comprehensive in its services and its effects, which brought changes in the structure of many communities and their organizational structures. They have significant impacts on the social systems and social relations, especially in the Arab societies, which are the focus of the globalized Western media, for many reasons: economical, political , cultural and social.
According to this perception, the Arab identity has become in an encounter with big challenges by the globalized media of trade and the media, which aims to achieve greater profits because of identity and its importance to the communities. This occurs par

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Publication Date
Mon Sep 01 2025
Journal Name
Thermal Science And Engineering Progress
Active mixing strategies for energy-efficient water dispensers: Comparative experimental study of impeller and bubble injection in hot climates
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