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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
Thu Apr 01 2021
Journal Name
Chaos, Solitons & Fractals
Modeling and analysis of an <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si7.svg"><mml:mrow><mml:mi>S</mml:mi><mml:msub><mml:mi>I</mml:mi><mml:mn>1</mml:mn></mml:msub><mml:msub><mml:mi>I</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:mi>R</mml:mi></mml:mrow></mml:math> epidemic model with nonlinear incidence and general recovery functions of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si8.svg"><mml:msub><mml:mi>I</mml:mi><mml:mn>1</mml:mn></mml:msub></mml:math>
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Publication Date
Sat Mar 26 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The effect of applying the electronic services system in the work of electronic banking: Applied research in a sample of Iraqi banks
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    The research aims to shed light on the impact of the application of the electronic services system on electronic banking activities in a sample of Iraqi banks, as investment in technology is the most important factor for the success and future growth of administrative companies in general, and banking in particular, as global economic developments in the field of Technology has led the majority of banking sectors in the world to undergo deep reforms and radical changes in the entity of their systems and mechanisms to confront competition and keep pace with economic changes, as the concept of banking services and its diversity changed with it, especially since persistence in the traditional approach no longer gi

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Publication Date
Fri Oct 25 2024
Journal Name
The Review Of Contemporary Scientific And Academic Studies
The Representation of Men and Women in the Black and White Streams of the Second Wave of Feminism: A Corpus Stylistic Analysis
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Publication Date
Thu Jun 30 2022
Journal Name
Iraq Journal Of Market Research And Consumer Protection
COMPARISON BETEEEN THE CONSUMPTION OF RED MEAT AND WHITE MEAT FOR ASAMPLE OF CITIZENS OF THE CITY OF BAGHDAD/ AN EXPLORATORY STUDY
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Three hundred Iraqi people participated in demographic and attitudes study about red and white meat consumption. The mean age of the participants was 50 SD ± 11 years (mean 30-72); 51% were females and 49% males, mostly in forties who lived ≥ 5 years in Baghdad. The results showed that 80% of individuals prefer red meat. A 90% of people prefer fresh meat compared to frozen and processed meat. A 60% of people buy meat from popular markets. Nearly 87% of respondents believe the improving of livestock sector is essential and 80% of people confirmed there are obstacles to development this sector. An 80% of participates thought the reasons of the high prices of local fresh meat is the lack of planning and support to livestock sector. A survey

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Determination of solar window for Baghdad city using pv system program
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Been using a pv system program to determine the solar window for Baghdad city . the solar window for any location can be determine by deviating left and right from the geographical south as well as deviation according to the amount of tilt angle with the horizon for fixed panel so that will not change the average of solar radiation incident over the whole year and this lead to help in the process of installation of fixed solar panel without any effect on annual output .the range of solar window for Baghdad city between two angles ( -8 - +8 ) degrees left to right of the geographical south and tilt angle that allowed for the horizon range between angles (21- 30) degrees so that the amount of solar radiation that falling on the solar pan

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Publication Date
Thu Dec 13 2018
Journal Name
International Journal Of Engineering &amp; Technology
Microwave Pyrolysis of Water hyacinth for Biochar Production Using Taguchi Method
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The manuscript should contain an abstract. The abstract should be self-contained and citation-free and should not exceed 200 words. The abstract should state the purpose, approach, results and conclusions of the work.  The author should assume that the reader has some knowledge of the subject but has not read the paper. Thus, the abstract should be intelligible and complete in it-self (no numerical references); it should not cite figures, tables, or sections of the paper. The abstract should be written using third person instead of first perso The fast microwave assisted pyrolysis (FMWAP) of water hyacinth (WH) for biochar production is investigated. Taguchi’s method was used to optimize FMWAP parameters. The effects of microwave

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Publication Date
Thu Jan 16 2020
Journal Name
Periodicals Of Engineering And Natural Sciences
Comparison of some reliability estimation methods for Laplace distribution using simulations
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In this paper, we derived an estimator of reliability function for Laplace distribution with two parameters using Bayes method with square error loss function, Jeffery’s formula and conditional probability random variable of observation. The main objective of this study is to find the efficiency of the derived Bayesian estimator compared to the maximum likelihood of this function and moment method using simulation technique by Monte Carlo method under different Laplace distribution parameters and sample sizes. The consequences have shown that Bayes estimator has been more efficient than the maximum likelihood estimator and moment estimator in all samples sizes

Publication Date
Wed Feb 01 2023
Journal Name
International Journal Of Revolution In Science And Humanity
Nonparametric Estimation of Failure Periods for Log Normal Distribution Using Bootstra
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A non-parametric kernel method with Bootstrap technology was used to estimate the confidence intervals of the system failure function of the log-normal distribution trace data. These are the times of failure of the machines of the spinning department of the weaving company in Wasit Governorate. Estimating the failure function in a parametric way represented by the method of the maximum likelihood estimator (MLE). The comparison between the parametric and non-parametric methods was done by using the average of Squares Error (MES) criterion. It has been noted the efficiency of the nonparametric methods based on Bootstrap compared to the parametric method. It was also noted that the curve estimation is more realistic and appropriate for the re

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Publication Date
Sat Feb 09 2019
Journal Name
Iraqi Journal Of Laser
Reconstruction of 3D Shape for an Object using Laser Scanning Triangulation
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This paper presents a method of designing and constructing a system capable of acquiring
the third dimension and reconstructs a 3D shape for an object from multi images of that object using
the principle of active optical triangulation. The system consists of an illumination source, a photo
detector, a movement mechanism and a PC, which is working as a controlling unit for the hard ware
components and as an image processing unit for the object multi view raw images which must be
processed to extract the third dimension. The result showed that the optical triangulation method
provides a rapid mean for obtaining accurate and quantitative distance measurements. The final
result's analysis refers to the necessity of usin

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Publication Date
Wed Sep 18 2024
Journal Name
Karbala International Journal Of Modern Science
Synthesis of ZnO: ZrO2 Nanocomposites Using Green Method for Medical Applications
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