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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
Fri Dec 31 2021
Journal Name
Political Sciences Journal
Populism in the Palestinian political discourse The Fatah and Hamas movements are a model
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Receipt Date:10/11/2021 Acceptance Date:29/12/2021 Publication Date:31/12/2021

Creative Commons LicenseThis work is licensed under a Creative Commons Attribution 4.0 International License.

The study aimed to clarify the conceptual explanations and the theoretical rooting of the concept of the populist phenomenon. And explore the political and cultural implications and connotations contained in populist political discourse. And to stand on the foundations and meanings on w

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Publication Date
Fri Sep 15 2023
Journal Name
Al-academy
Publicizing the survey image in local consumer protection the mission program is a model
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The investigative film is part of the documentary films and is considered one of the important films that have a high viewership by the recipient, which is of great importance in transmitting information and contributing to creating awareness of the community through the advertising function performed by the cinematic image, as the researcher addresses the concept of advertising and its development through the time stages. And advertising functions. Then the researcher dealt in his research with the cinematic technical elements that contribute to the success of the investigative advertising work, such as camera movements, music, sound effects, dialogue ... etc., which enrich the investigative picture with realism and the flow of informat

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Publication Date
Mon Jun 01 2020
Journal Name
Al-khwarizmi Engineering Journal
Developing a Prosthesis Design using A Gearbox to Replicate the Human Hand Mechanism
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Prosthetic is an artificial tool that replaces a member of the human frame that is  absent because of ailment, damage, or distortion. The current research activities in Iraq draw interest to the upper limb discipline because of the growth in the number  of amputees. Thus, it becomes necessary to increase researches in this subject to help in reducing the struggling patients.  This paper describes the design and development of a prosthesis for people able and wear them from persons who have amputation in the hands. This design is composed of a hand with five fingers moving by means of a gearbox ism mechanism. The design of this artificial hand has 5 degrees of freedom. This artificial hand works based on the principle of &n

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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Suggestive Framework for Applying Performance and Programs Budget in Iraqi Government Units Environment
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Abstract

This research  aims to reform the Iraqi public budget through going into the challenges the budget faces in applying item-line budget in its preparation, implementation and control; which encourage extravagance and waste instead of rationalizing expenditures. This  is shown in the data analysis of Federal public budget laws in Iraq for the years from 2005 till 2013; there was a continuous increase in the aggregate public expenditures in the public budget for the years previously mentioned, as the public expenditures growth has reached into the percent 284.71% in 2013. In addition the public budget for these years (2005-2013) is being prepared with planned deficit without confirming that

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Publication Date
Fri Apr 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison Between Classic Local Least Estimatop And Bayesian Methoid For Estimating Semiparametric Logistic Regression Model
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Semi-parametric models analysis is one of the most interesting subjects in recent studies due to give an efficient model estimation. The problem when the response variable has one of two values either 0 ( no response) or one – with response which is called the logistic regression model.

We compare two methods Bayesian and . Then the results were compared using MSe criteria.

A simulation had been used to study the empirical behavior for the Logistic model , with  different sample sizes and variances. The results using represent that the Bayesian method is better than the   at small samples sizes.

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Publication Date
Thu Nov 21 2019
Journal Name
Journal Of Engineering
A Neural Networks based Predictive Voltage-Tracking Controller Design for Proton Exchange Membrane Fuel Cell Model
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In this work, a new development of predictive voltage-tracking control algorithm for Proton Exchange Membrane Fuel Cell (PEMFCs) model, using a neural network technique based on-line auto-tuning intelligent algorithm was proposed. The aim of proposed robust feedback nonlinear neural predictive voltage controller is to find precisely and quickly the optimal hydrogen partial pressure action to control the stack terminal voltage of the (PEMFC) model for N-step ahead prediction. The Chaotic Particle Swarm Optimization (CPSO) implemented as a stable and robust on-line auto-tune algorithm to find the optimal weights for the proposed predictive neural network controller to improve system performance in terms of fast-tracking de

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Publication Date
Thu Jun 01 2017
Journal Name
Nuclear Physics A
Alpha-cluster preformation factor within cluster-formation model for odd-A and odd–odd heavy nuclei
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Publication Date
Sun May 10 2015
Journal Name
Al-academy
Performing processors of view between impressionism & superrealism (A comparative analysis): فريد خالد علوان
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Addressed the problem of the research is marked: (Performing processors for the time between Impressionism and superrealism) the concept of time and how to submit artwork. The search came in four sections: general framework for research and identified the research problem and the need for him. With an indication of the importance of his presence. Then determine the research objectives of (detection processors performing to the concept of time in works of art in each of Impressionism and superrealism. And a comparison between them to reveal similarities and differences), followed by the establishment of boundaries Find three (objectivity, the temporal and spatial) were then determine the terms related to the title. Then provide the theore

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Publication Date
Mon Dec 01 2014
Journal Name
2014 Ieee Symposium On Differential Evolution (sde)
Comparative analysis of a modified differential evolution algorithm based on bacterial mutation scheme
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A new modified differential evolution algorithm DE-BEA, is proposed to improve the reliability of the standard DE/current-to-rand/1/bin by implementing a new mutation scheme inspired by the bacterial evolutionary algorithm (BEA). The crossover and the selection schemes of the DE method are also modified to fit the new DE-BEA mechanism. The new scheme diversifies the population by applying to all the individuals a segment based scheme that generates multiple copies (clones) from each individual one-by-one and applies the BEA segment-wise mechanism. These new steps are embedded in the DE/current-to-rand/bin scheme. The performance of the new algorithm has been compared with several DE variants over eighteen benchmark functions including sever

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Publication Date
Sun Mar 13 2011
Journal Name
Baghdad Science Journal
Using of Rustumiya sewage water for irrigation:1- its effect on some soil properties and corn growth
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This study is conducted to investigate the validity of using different levels of Rustumiya sewage water for irrigation and their effects on corn growth and some of the chemical properties of the soil such as electrical conductivity and soil pH in extract soil paste , the micro nutrient content in soil and plant which are ( Fe , Mn , Zn , Cu , Cd , Pb ). Three levels of sewage water ( 0 , 50 , 100 )% in two stages were used ,the three levels of wastewater ( without soil fertilization ) were used in the first stage , Where 80 Kg N /D+50Kg P2O5 /D was added to the soil as fertilizer in the control (0%) treatment and 40 Kg N/D+25Kg P2O5/D were added to 50 and 100% levels in the second stage .Corn seeds were planted in 12kg plastic pots in Com

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