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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
Mon May 16 2016
Journal Name
Far East Journal Of Mathematical Sciences (fjms)
MINIMIZING WAITING TIMES USING MULTIPLE FUZZY QUEUEING MODEL WITH SUPPLY PRIORITIES
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Publication Date
Mon Oct 22 2018
Journal Name
Journal Of Economics And Administrative Sciences
Using simulation to compare between parametric and nonparametric transfer function model
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In this paper, The transfer function model in the time series was estimated using different methods, including parametric Represented by the method of the Conditional Likelihood Function, as well as the use of abilities nonparametric are in two methods  local linear regression and cubic smoothing spline method, This research aims to compare those capabilities with the nonlinear transfer function model by using the style of simulation and the study of two models as output variable and one model as input variable in addition t

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Publication Date
Thu Sep 01 2022
Journal Name
Iraqi Journal Of Physics
Calculation of the Magnetic Dipole and Electric Quadrupole Moments of some Sodium Isotopes using Shell Model with Skyrme Interaction
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         In the present work, the magnetic dipole and electric quadrupole moments for some sodium isotopes have been calculated using the shell model, considering the effect of the two-body effective interactions and the single-particle potentials. These isotopes are; 21Na (3/2+), 23Na (3/2+), 25Na (5/2+), 26Na (3+), 27Na (5/2+), 28Na (1+) and, 29Na (3/2+). The one-body transition density matrix elements (OBDM) have been calculated using the (USDA, USDB, HBUMSD and W) two-body effective interactions carried out in the sd-shell model space. The sd shell model space consists of the active 2s1/2, 1d5/2,

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Publication Date
Wed Feb 23 2022
Journal Name
Iraqi Journal Of Agricultural Sciences
AN ECONOMIC ANALYSIS OF SOME FACTORS AFFECTING IN MARKETING EFFICIENCY OF DRY ONION CROP USING THE TOBIT REGRESSION MODEL
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The study was aimed to evaluate the marketing efficiency of dry Onion crop in Salah al-Deen, as estimate the impact of some quality and quantity factors in the efficiency of marketing process of crop using Tobit regression model. The average marketing efficiency of the research sample was 71.3686%. The marketing margins differed according to the marketing channel followed in marketing the crop. The qualitative and quantitative variables in the model are productivity, family size, distance from the market, educational level. The estimated model revealed that a variable productivity is the most important and influential in marketing efficiency, followed by the variable of the distance between the farm and the market, then the variable

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Publication Date
Wed Feb 23 2022
Journal Name
Iraqi Journal Of Agricultural Sciences
AN ECONOMIC ANALYSIS OF SOME FACTORS AFFECTING IN MARKETING EFFICIENCY OF DRY ONION CROP USING THE TOBIT REGRESSION MODEL
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The study was aimed to evaluate the marketing efficiency of dry Onion crop in Salah al-Deen, as estimate the impact of some quality and quantity factors in the efficiency of marketing process of crop using Tobit regression model. The average marketing efficiency of the research sample was 71.3686%. The marketing margins differed according to the marketing channel followed in marketing the crop. The qualitative and quantitative variables in the model are productivity, family size, distance from the market, educational level. The estimated model revealed that a variable productivity is the most important and influential in marketing efficiency, followed by the variable of the distance between the farm and the market, then the variable

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Publication Date
Wed Apr 12 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Synthesis, Characterization and Study Biological Activity of Some New 1, 3, 4-Thiadiazole and Pyrazolone Derivatives Containing Indole Ring
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This work involves synthesis and characterization of some new 1, 3, 4-thiadiazole or pyrazoline derivatives heterocyclic containing indole ring. The new 2-amino-1, 3, 4-thiadiazole derivatives [IV] and [V] a, b were synthesized by cyclization reaction of 2-methyl-1H-indole-carbothiosemicarbazide [III] in H2SO4 acid or by reaction of indole-3-acetic acid or indole-3-butanoic acid with thiosemicarbazide in the presence of phosphorous oxychloride, respectively. Amide derivatives [VI]-[VIII] were synthesized by the reaction equimolar of 2-amino-1, 3, 4-thiadiazoles and (acetyl chloride, benzoyl chloride, anisoyl chloride and heptanoyl chloride) in DMF and pyridine as accepter. The new pyrazolone derivatives [XI] a, b were synthesized from heati

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Publication Date
Wed May 15 2024
Journal Name
International Journal Of Religion
(The Importance of Knowledge and Work in Islamic Thought) A Study of the Stages of Spiritual Purification According to Imam Al-Ghazali
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Science occupies great importance in Islamic thought. Science and learning are considered an essential part of Islamic teachings, and this importance appears in several aspects,Among them is thatScience as a means of understanding religion :Science is a means of understanding the teachings of the Islamic religion. Islam encourages thinking and rational research to understand the Holy Quran and the Sunnah of the Prophet, enabling Muslims to direct their lives and actions in accordance with the directives of their religion,And also to encourageResearch :Islam encourages scientific research and the use of reason in understanding the nature of the universe and God’s signs in it. Muslims are encouraged to study the natural and social s

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Publication Date
Sat Jun 06 2020
Journal Name
Journal Of The College Of Education For Women
Spatial Analysis of Soil Characteristics and its Effect on Determining the Susceptibility of lands of the RasheedRegion: A Study in Soil Geography
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Twelve pends were selected and distributed on three verticals transects paths on the Tigers river in Al Rasheed county.Passing through land covers, that classified and covers the whole region. Based on the 8 Landsat of the year 2015. It was oriental classified by using Erdas 10.2 . The pedons were distributed on the area of each varicty of these classes. the series of soil according of the transect series (DW74,MMg,DMu6 , Df96) respectively were represented P1 , P2 , P3 , P4  .

The second transits series(DM97,MM5,DM96,DF115) respectively were  represented P5 , P6 , P7 , P8  .The third  transits series(DM46,MMg,MF12,MM11) re

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Strategic orientation and its reflection on the Learning organization: Survey study of a sample of Makers decision the Iraqi Ministry of Communications
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The current research focuses on the extent to which the strategic orientation(entrepreneurial orientation, customer orientation, technology orientation, learning orientation, and investment orientation) affects the learning organization (building common vision, systemic thinking, personal dominance, mental models, team learning)The first hypothesis to test the connection relation between research variables and The second hypothesis was to test the relationship between these variables. In order to ascertain the validity of the hypotheses, the research was based on a questionnaire questionnaire prepared according to a number of In addition to building a fifth sub-variable for the strategic orientation (investment orientation) based

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The role of marketing recovery in improving the organization's reputation An applied study of a sample of private bank managers in Baghdad
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This research aims to know and the role of the marketing recovery dimensions in improving the organization's reputation through an exploratory study of private banks in the city of Baghdad. The aim of the research is to define the role of the marketing recovery through its dimensions (compensation, apology, speed of response, assistance and problem solving), in improving the organization's reputation, as the research will attempt to provide a theoretical framework for the dimensions studied through the most important of what researchers presented and then conduct the applied aspect of the research. Data were collected using a questionnaire-based survey consisting of 35 questions and distributed to 110 managers of private banks in

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