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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
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
Thu Nov 21 2024
Journal Name
F1000research
Comparison of the severity of urinary tract infections between Metformin and SGL2 Inhibitors among Iraqi Type 2 Diabetics.
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Background Many antidiabetic medications with distinct modes of action are available, The sodium glucose cotransporter-2 (SGLT-2) inhibitors are among the most recent oral antihyperglycemic medications. The American Diabetes Association recommends metformin, a biguanide medication, as the first option for oral control of type 2 diabetes because it has demonstrated promise in this regard. Aim of the study To evaluate and compare the effects of metformin and SGLT-2 inhibitors on general urine parameters in T2DM patients from Iraq. Method a prospective cohort study where 101 adult patients of both sexes aged under 70 years and newly diagnosed with T2DM, patients were divided into two groups, Metformin group (n=52), where metformin was p

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Publication Date
Wed Nov 03 2021
Journal Name
Al-ghary Journal Of Economic And Administrative Sciences
The Role of Marketing Vigilance in Analyzing the Strategic Position of Tourism Organization: A Survey Study of the Opinions of a Sample of Travel and Tourism Companies
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The study aims at studying and analyzing the subject of marketing vigilance as it is one of the modern approaches in the marketing field that can be used to face changes in the competitive and strategic environment and that represents quick reactions on the part of the institution to ensure its survival and distinctiveness other aims are: Consolidating the strength of the marketing organization and its success continuously, represented by changes in the market share, awareness of the institution's position in the market and its relations with competing tourism companies, diversification of tourism services, as well as an analysis of the competitive strategic position of tourism institutions for the purpose of conducting a r

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Publication Date
Wed Dec 30 2015
Journal Name
College Of Islamic Sciences
Arrows of Kurdish scholars in the service of the Sunnah of Imam Majd al-Din Ibn al-Atheer al-Jazari (544_606): A model
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This research is a modest effort to talk about the great world of ancient lineage, Imam Majd al-Din Abu Saadat, known as Ibn al-Atheer island, through the statement of his name, surname, nickname, family, elders and his pupils and his most important works.
It also deals with the modern research on his famous book in the field of modern science called (the end in the strange talk and impact), which is one of the most wonderful books of modern and especially the strange talk, through the scientific effort of the Imam and the importance of the book and methodology, and the most prominent aspects of the service and care of Ibn Al Atheer For the modern stranger, which boils down to two aspects:
First: the linguistic rooting of the stran

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Publication Date
Tue Dec 30 2014
Journal Name
College Of Islamic Sciences
Investigations in the sanctity of divine texts and their composition: (Comparative study between the Quran and the Torah)
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The research deals with an important issue that many people are working on, namely the sanctification of the texts on which the timings of the time and the different conditions of the place took place. Do not live up to the ranks of perfection and perfection, and every effort has explanations according to the mind machine, which is not protected by infallibility from error. The great downfall is to put these intellectual efforts in the Bible without separating them from the Word of God. The situation and the place on the adherents of a religion and mixed with the trick of the average individual only to be subject to the words of the teachers of Sharia and docility.

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Engineering
Design of a PID-Lead Compensator for a Twin Rotor Aerodynamic System (TRAS)
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This paper deals with a Twin Rotor Aerodynamic System (TRAS). It is a Multi-Input Multi-Output (MIMO) system with high crosscoupling between its two channels. It proposes a hybrid design procedure that combines frequency response and root locus approaches. The proposed controller is designated as PID-Lead Compensator (PIDLC); the PID controller was designed in previous work using frequency response design specifications, while the lead compensator is proposed in this paper and is designed using the root locus method. A general explicit formula for angle computations in any of the four quadrants is also given. The lead compensator is designed by shifting the dominant closed-loop poles slightly to the left in the s-plane. This has the effect

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Engineering
Design of a PID-Lead Compensator for a Twin Rotor Aerodynamic System (TRAS)
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This paper deals with a Twin Rotor Aerodynamic System (TRAS). It is a Multi-Input Multi-Output (MIMO) system with high crosscoupling between its two channels. It proposes a hybrid design procedure that combines frequency response and root locus approaches. The proposed controller is designated as PID-Lead Compensator (PIDLC); the PID controller was designed in previous work using frequency response design specifications, while the lead compensator is proposed in this paper and is designed using the root locus method. A general explicit formula for angle computations in any of the four quadrants is also given. The lead compensator is designed by shifting the dominant closed-loop poles slightly to the left in the

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Publication Date
Sat Oct 01 2022
Journal Name
Baghdad Science Journal
Design of a Simple Dust Removal System for a Solar Street Light System
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      Dust and bird residue are problems impeding the operation of solar street lighting systems, especially in semi-desert areas, such as Iraq. The system in this paper was designed and developed locally using simple and inexpensive materials. The system runs automatically. It Connects to solar panels used in solar street lighting, and gets the required electricity from the same solar system. Solar panels are washed with dripping water in less than half a minute by this system. The cleaning period can also be controlled. It can also control, sensing the amount of dust the system operates. The impact of different types of falling dust on panels has also been studied. This was collected from different winds and studied their impact o

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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
Sun Mar 01 2020
Journal Name
Iraqi Journal Of Physics
Chaotic features of energy spectrum in 68Ge Nucleus Using the Nuclear Shell Model
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   Chaotic features of nuclear energy spectrum in 68Ge nucleus are investigated by nuclear shell model. The energies are calculated through doing shell model calculations employing the OXBASH computer code with effective interaction of F5PVH. The 68Ge nucleus is supposed to have an inert core of 56Ni with 12 nucleons (4 protons and 8 neutrons) move in the f5p-model space ( and ). The nuclear level density of considered classes of states is seen to have a Gaussian form, which is in accord with the prediction of other theoretical studies. The statistical fluctuations of the energy spectrum (the level spacing P(s) and the Dyson-Mehta (or statistics) are well described by the Gaussian orthogonal ens

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