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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 Oct 26 2024
Journal Name
Zac Conference Series: Social Sciences And Humanities
A Comparative Study of Postwar Literature (Iranian Defense and Vietnam’s War) a Komunyakaa’s and Aminpour’s Poems
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The comparative study tries to find the common points in two different authors’ works and in this kind of studying so many other common but the hidden points may be revealed. Postwar literature is somehow one of the best literary genres for finding the common factors and features that the poets have tried to present in their works elements such as desire to be winner, cruelty, inhumanity, and absurdity of the war.  The Iranian poet late Qaisar Aminpour(1961-2007)  and Yusef Komunyakaa ( 1947) from  Bogalusa, Louisiana, are among the great American and Iranian  poets whose works so many times have been  interpreted and analyzed. The finding the outstanding and the most important points and themes in the postwar poems of these

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Publication Date
Wed Jul 01 2015
Journal Name
Al–bahith Al–a'alami
The Position of the Oil Press about the World Oil Industry / OAPEC Bulletin 2011-2012 as a Model
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This research deals with the attitude of oil press towards oil industry in the world and the extent of their concerns with the stages of oil industry relating to the abundance of oil and natural gas, as it is an international strategic and complementary industry. The researcher uses the survey method for content analysis of the initial article and the press news for two: years (2011-2012). The results if the study are as follows
1- Oil press is concerned with developing and the stages of the Arabic oil industry in the interest of OAPEC in the first place.
2- It is concerned with exploring, extracting, and marketing oil in the first place, then with refining operations in refineries and petrochemical plants in the second place, an

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Publication Date
Wed Mar 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Expired Colxacillin, Amoxicillin, and Ceflaxin Drugs as Inhibitors for Low Carbon Steel Corrosion in Sodium Chloride
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The ability to inhibit corrosion of low carbon steel in a salt solution (3.5%NaCl) has been checked with three real expired drugs (Cloxacillin, Amoxicillin, Ceflaxin) with variable concentrations (0, 250, 500, 750) mg/L were examined in the weight loss. The inhibition efficiency of the Cloxacillin 750 mg/L showed the highest value (82.8125 %) and the best inhibitor of the rest of the antibiotics. The different concentrations of Cloxacillin drug (0, 250, 500, 750) mg/L and temperature (25, 35, 45, 55) oC were studied as variables with potentiodynamic polarization, Scanning Electron Microscopy (SEM) for surface morphology and electrochemical impedance spectroscopy (EIS) depending on current values and the resistance of charge to

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Publication Date
Fri Dec 01 2023
Journal Name
Bulletin Of Electrical Engineering And Informatics
A comparative study of Gaussian mixture algorithm and K-means algorithm for efficient energy clustering in MWSN
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Wireless sensor networks (WSNs) represent one of the key technologies in internet of things (IoTs) networks. Since WSNs have finite energy sources, there is ongoing research work to develop new strategies for minimizing power consumption or enhancing traditional techniques. In this paper, a novel Gaussian mixture models (GMMs) algorithm is proposed for mobile wireless sensor networks (MWSNs) for energy saving. Performance evaluation of the clustering process with the GMM algorithm shows a remarkable energy saving in the network of up to 92%. In addition, a comparison with another clustering strategy that uses the K-means algorithm has been made, and the developed method has outperformed K-means with superior performance, saving ener

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Publication Date
Fri Sep 17 2021
Journal Name
Al-kindy College Medical Journal
Single Layer Extra-Mucosal Versus Double Layer Intestinal Anastomosis for Colostomy Closure: A Prospective Comparative Study
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Background: The main objective was to compare the outcome of single layer interrupted extra-mucosal sutures with that of double layer suturing in the closure of colostomies.

Subjects and Methods: Sixty-seven patients with closure colostomy were assigned in a prospective randomized fashion into either single layer extra-mucosal anastomosis (Group A) or double layer anastomosis (Group B). Primary outcome measures included mean time taken for anastomosis, immediate postoperative complications, and mean duration of hospital stay. Secondary outcome measures assessed the postoperative return of bowel function, and the overall mean cost. Chi-square test and student t-test did the statistical analysis..

Resu

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Publication Date
Fri Jul 29 2022
Journal Name
Journal For Vascular Ultrasound
A Comparative Study of the Right and Left Carotid Arteries in Relation to Age for Patients With Diabetes and Hypertension
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Introduction:

Age, hypertension, and diabetes can cause significant alterations in arterial structure and function, including changes in lumen diameter (LD), intimal-medial thickness (IMT), flow velocities, and arterial compliance. These are also considered risk markers of atherosclerosis and cerebrovascular disease. A difference between right and left carotid artery blood flow and IMT has been reported by some researchers, and a difference in the incidence of nonlacunar stroke has been reported between the right and left brain hemispheres. The aim of this study was to determine whether there are differences between the right and left common carotid arteries and internal carotid arteries in patient

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Publication Date
Thu Jun 25 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn: 1683 - 3597 , E-issn : 2521 - 3512)
Evaluating the Clinical Outcomes of Three Medication Regimens for Treating a Sample of Iraqi Persistent Asthmatic patients
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Abstract     Asthma is a complex disease defined by chronic airway inflammation and airflow limitation causing variable respiratory symptoms which include shortness of breath (SOB), wheezing, chest tightness and cough. Asthma guidelines advocate adding a second long acting bronchodilator to medium doses of inhaled corticosteroids (ICS) rather using high doses of ICS alone to control moderate to severe persistent asthma. The aim of this study was to evaluate the clinical outcomes of three medication regimens indicated for Iraqi patients suffering from persistent asthma.      This study was interventional randomized clinical study conducted on a sample of adult Iraqi asthmatic patients in Baghdad City. The study com

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Publication Date
Thu Jun 25 2020
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Evaluating the Clinical Outcomes of Three Medication Regimens for Treating a Sample of Iraqi Persistent Asthmatic patients
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Abstract

    Asthma is a complex disease defined by chronic airway inflammation and airflow limitation causing variable respiratory symptoms which include shortness of breath (SOB), wheezing, chest tightness and cough. Asthma guidelines advocate adding a second long acting bronchodilator to medium doses of inhaled corticosteroids (ICS) rather using high doses of ICS alone to control moderate to severe persistent asthma. The aim of this study was to evaluate the clinical outcomes of three medication regimens indicated for Iraqi patients suffering from persistent asthma. 

    This study was interventional randomized clinical study conducted on a sample of adult Iraqi asthm

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Publication Date
Mon Jun 16 2025
Journal Name
Al–bahith Al–a'alami
Media separation: The Relationship of Arab Immigrants with the Media of the Countries of Diaspora (Sweden as a model) (A Research Derived from PhD Dissertation)
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The research seeks to study the subject (Media separation: the Relationship of Arab Immigrants with the Media of the Countries of Diaspora/ Sweden as a model). Where this phenomenon, "problem" has not been subjected to an in-depth study to find out the causes of this media separation and its repercussions on the immigrant, whether in the problem of integration, or his opportunity to work, or adapt to live in the new society.

Separation is a kind of word that is rarely used in Arabic media studies, relevant, sometimes, to the meaning of “refraining from watching TV or listening to the radio or reading newspapers”. Sometimes, it means “not tuning to or using any form of media like radios or newspapers to be updated about what

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Publication Date
Sun Jun 07 2009
Journal Name
Baghdad Science Journal
The adsorption-desorption process as a method for separation of nitrogen-carbon dioxide gas mixture using activated carbon
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Gas adsorption phenomenon on solid surface has been used as a mean in separation and purification of gas mixture depending on the difference in tendencies of each component in the gas mixture to be adsorbed on the solid surface according to its behaviour. This work concerns to study the possibilities to separate the gas mixture using adsorption-desorption phenomenon on activated carbon. The experimental results exhibit good separation factor at temperature of -40 .

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