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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
Wed Feb 05 2020
Journal Name
Political Sciences Journal
Frustrations of sectarian coexistence and mechanisms to activate peaceful coexistence: Iraq as a model
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Abstract The study aimed at demonstrating the reality of sectarian coexistence in Iraq, which was characterized by the tolerance and coercion caused by the successive government policies to govern Iraq and to this day. The study was based on the hypothesis that coexistence between Islamic sects in Iraq can be achieved as long as there are strong bonds linking its components, and these bonds can produce coexistence between the sects based on peace. The study concluded that the hypothesis is correct, in addition to drawing a set of observations aimed at identifying weaknesses for advancing them through the adoption of mechanisms that address these weaknesses to yield towards a genuine peaceful coexistence among Islamic sects in Iraq.

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Publication Date
Fri Mar 01 2024
Journal Name
الذكوات البيض
The problem of employing political discourse and its role in promoting community peace: Iraq as a model
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After 2003, Iraq witnessed new challenges represented by the predominance of sectarian discourses, hatred and extremism at the expense of moderate political discourse and the predominance of sub-affiliations and external agendas at the expense of national affiliation, which led to the creation of an unsafe or stable environment dominated by the character of violence and terrorism. Moderate discourse would work to fuse sub-affiliations into one melting pot in which it would be the first loyalty to the homeland and not to the tribe, party or sect... Etc., and this in turn will contribute to promoting peaceful coexistence between the various other sub-affiliations within the framework of one community construction

Publication Date
Fri Feb 28 2025
Journal Name
Moroccan Journal Of Chemistry
Design, Synthesis, and Biological Evaluation of new sulfonamides derived from 2-Aminopyridine: Molecular docking, POM analysis, and identification of the pharmacophore sites
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New series of imidazole[1,2-a]pyridine-sulfonamides was designed and synthesized from 2-aminopyridine, which was reacted with p-bromo phenacyl bromide in the present of MgO to produce the corresponding imidazole[1,2-a]pyridine, which was then reacted with chlorosulfonic acid to produce 2-(4-bromophenyl)imidazole[1,2-a]pyridine-3-sulfonyl chloride [2]. Following that, treatment of (2) with different amines using the grand method to generate imidazole [1,2-a] pyridine sulfonamides. All the synthesized compounds have been characterized by FTIR, 1HNMR and 13CNMR and C.H.N analysis. The DFT, POM analysis and molecular docking were carried out on for all final compounds to investigate drug like attributes, and the results revealed showed that the

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Publication Date
Wed May 18 2016
Journal Name
Al-academy
The Application of Experimentation in the Iraqi theatre shows "Othello in the Kitchen" As a model: عادل كريم سالم
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The researcher tackles the most outstanding conditions of experimentation, the importance of the study lies in being helpful to the workers in the field of theatre in general and directors in particular which the conditions of experimentation that should be taken.The study aims at knowing the experimental basis which the director (Sami Abdulhamid) followed in the realization of this.The researcher tackles in the First inquiry the concept of experimentation and the second tackles the conditions of experimentation.In the methodology of study the researcher analyzed the show of the "Othello in the Kitchen" and comes up to the following: 1. the dhows has cone with the nature of the previous shows experienced the methods that were not familia

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Publication Date
Thu Sep 30 2010
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
USING ALUMINUM REFUSE AS A COAGULANT IN THE COAGULATION AND FLIOCCULATION PROCESSES
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The present work aims to study the efficiency of using aluminum refuse, which is available locally (after dissolving it in sodium hydroxide), with different coagulants like alum [Al2 (SO4)3.18H2O], Ferric chloride FeCl3 and polyaluminum chloride (PACl) to improve the quality of water. The results showed that using this coagulant in the flocculation process gave high results in the removal of turbidity as well as improving the quality of water by precipitating a great deal of ions causing hardness. From the experimental results of the Jar test, the optimum alum dosages are (25, 50 and 70 ppm), ferric chloride dosages are (15, 40 and 60 ppm) and polyaluminum chloride dosages were (10, 35 and 55 ppm) for initial water turbidity (100, 500 an

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Publication Date
Sun May 01 2022
Journal Name
Songklanakarin J. Sci. Technol.
Molecular identification of three novel species of Ganoderma from different habitats in Mosul, Iraq
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Reishi Mushroom, Ganoderma, is considered one of important wood-decaying medicinal mushrooms. This study aimed to identify three samples of this genus in Mosul city in February and April 2019. Three species of Ganoderma were collected from three various trees including Eucalyptus, Morus, and Olea (olive) in Mosul City, Northern Iraq. Their identifications and their DNA sequences were genetically identified by using PCR techniques according to detect nuclear ribosomal internal transcribed spacer (ITS) regions. Results exhibited the finding of Ganoderma resinaceum, Ganoderma applanatum, and Ganoderma sp. This study is first attempt to identify Reishi Mushroom by molecular methods in Iraq. Thus, the current study is considered new good d

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Publication Date
Thu Dec 01 2022
Journal Name
Advances In Cancer Biology - Metastasis
CX3CL1 as potential immunotherapeutic tool for bone metastases in lung cancer: A preclinical study
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Publication Date
Sat Jul 01 2017
Journal Name
Al–bahith Al–a'alami
A Dubbed Turkish Drama and their Effects of the Behavior of Algerian Women: A Survey Study of a Sample of Women – The City of Mesila is a Model
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The study aims to identify the effects of dubbed Turkish drama on the public through the application of a sample of the views of women. The study also attempts to monitor the causes and motives due to the act of observation and to identify the various effects of this act. In order to achieve these goals, the researcher relies on the descriptive approach in addition to the questionnaire and interviews to collect data. It ends with a number of results such as: The study aims to identify the effects of dubbed Turkish drama on the public through the application of a sample of the views of women. The study also attempts to monitor the causes and motives due to the act of observation and to identify the various effects of this act. In ord

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Publication Date
Wed May 01 2024
Journal Name
Journal Of Physics: Conference Series
A modified ARIMA model for forecasting chemical sales in the USA
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Abstract<p>model is derived, and the methodology is given in detail. The model is constructed depending on some measurement criteria, Akaike and Bayesian information criterion. For the new time series model, a new algorithm has been generated. The forecasting process, one and two steps ahead, is discussed in detail. Some exploratory data analysis is given in the beginning. The best model is selected based on some criteria; it is compared with some naïve models. The modified model is applied to a monthly chemical sales dataset (January 1992 to Dec 2019), where the dataset in this work has been downloaded from the United States of America census (www.census.gov). Ultimately, the forecasted sales </p> ... Show More
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Publication Date
Fri Dec 29 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Smartphone -Based Model for Human Activity Recognition
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Activity recognition (AR) is a new interesting and challenging research area with many applications (e.g. healthcare, security, and event detection). Basically, activity recognition (e.g. identifying user’s physical activity) is more likely to be considered as a classification problem. In this paper, a combination of 7 classification methods is employed and experimented on accelerometer data collected via smartphones, and compared for best performance. The dataset is collected from 59 individuals who performed 6 different activities (i.e. walk, jog, sit, stand, upstairs, and downstairs). The total number of dataset instances is 5418 with 46 labeled features. The results show that the proposed method of ensemble boost-based classif

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