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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 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
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
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
Mon Feb 20 2012
Journal Name
North Africa Technical Conference And Exhibition
Comprehensive Model for Flash Calculations of Heavy Oils Using the Soave - Redlich - Kwong Equation of State
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Abstract<p>One of the main techniques to achieve phase behavior calculations of reservoir fluids is the equation of state. Soave - Redlich - Kwong equation of state can then be used to predict the phase behavior of the petroleum fluids by treating it as a multi-components system of pure and pseudo-components. The use of Soave – Redlich – Kwon equation of state is popular in the calculations of petroleum engineering therefore many researchers used it to perform phase behavior analysis for reservoir fluids (Wang and Orr (2000), Ertekin and Obut (2003), Hasan (2004) and Haghtalab (2011))</p><p>This paper presents a new flash model for reservoir fluids in gas – oil se</p> ... Show More
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Publication Date
Wed Jan 01 2025
Journal Name
Aip Conference Proceedings
Enhanced aerodynamics for sport cars using inverted wings: A comprehensive review
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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Detection capability Alttafaria for some materials using a bacterial mutagenesis system
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Tested effective Alttafaria some materials used for different purposes, system a bacterial mutagenesis component of three bacterial isolates belonging to different races and materials tested included drug Briaktin

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Publication Date
Tue Jan 01 2008
Journal Name
Journal Of Engineering
USING FUZZY LOGIC CONTROLLER FOR A TWO- TANK LEVEL CONTROL SYSTEM
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This paper presents a fuzzy logic controller for a two-tank level control system, which is a process with a dead time. The fuzzy controller is a proportional-integral (PI-like) fuzzy controller which is suitable for steady state behavior of the system. Transient behavior of the system was improved without the need for a derivative action by suitable change in the rule base of the controller. Simulation results showed the step response of the two-tank level control system when this controller was used to control this plant and the effect of the dead time on the response of the system.