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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
Tue Nov 01 2022
Journal Name
Journal Of Engineering
Artificial Neural Network Model for Wastewater Projects Maintenance Management Plan
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Wastewater projects are one of the most important infrastructure projects, which require developing strategic plans to manage these projects. Most of the wastewater projects in Iraq don’t have a maintenance plan. This research aims to prepare the maintenance management plan (MMP) for wastewater projects. The objective of the research is to predict the cost and time of maintenance projects by building a model using ANN. The research sample included (15) completed projects in Wasit Governorate, where the researcher was able to obtain the data of these projects through the historical information of the Wasit Sewage Directorate. In this research artificial neural networks (ANN) technique was used to build two models (cost

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Publication Date
Thu Jun 01 2023
Journal Name
International Journal Of Electrical And Computer Engineering (ijece)
An optimized deep learning model for optical character recognition applications
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The convolutional neural networks (CNN) are among the most utilized neural networks in various applications, including deep learning. In recent years, the continuing extension of CNN into increasingly complicated domains has made its training process more difficult. Thus, researchers adopted optimized hybrid algorithms to address this problem. In this work, a novel chaotic black hole algorithm-based approach was created for the training of CNN to optimize its performance via avoidance of entrapment in the local minima. The logistic chaotic map was used to initialize the population instead of using the uniform distribution. The proposed training algorithm was developed based on a specific benchmark problem for optical character recog

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Publication Date
Sun Dec 30 2001
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Analyzing and Optimizing Bits Performance in Three Iraqi Oil-Fields
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Publication Date
Fri Jul 01 2016
Journal Name
Al–bahith Al–a'alami
A Semiotic Approach to the Analysis of the News Story
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This study attempts to provide an approach analysis for the news, depending on the bases and principles which conceptuality semiotic researchers of this field first of them «A. J. Gremas» for the theory of «narrative discourse analysis», to more clarify we tried to apply it on a published press- news, to concludes the most important steps and methods that are necessary to follows gain more understanding of the press- news.

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Publication Date
Wed May 17 2023
Journal Name
College Of Islamic Sciences
A stylistic vision of the objection in the Quranic discourse
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The modern stylistic lesson has become more committed to the scientific limits in which it believed, and more confident in itself, and it is no longer just a scientific procedure that helps other curricula and sciences that preceded it.

Based on this, our modest research ((a stylistic vision of the objection in the Quranic discourse)) arose to explore an artistic rhetorical phenomenon that was included in the Holy Quran text. ; Because analysis is a situation that allows us to see a lot and absorb the stranger more clearly.

And since the horizontal arrangement of the linguistic elements in which stylistically undistinguished elements meet with distinct ones, the other trend has emerged that believes that the stylistic dis

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Publication Date
Tue Jun 30 2015
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Improving Treatment Performance of Dissolved Air Flotation System by Using Ionic Liquids as Surfactants
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The effect of three ionic liquids viz., 1-hexyl-3-methylimidazolium tetrafluoroborate (ILE), 1-hexyl-3-metylimidazolium hexafluorophosphate (ILF) and 1-octyl-3-methylimidazolium tetrafluoroborate (ILG) when used as surfactants on the performance of dissolved air floatation (DAF) was investigated.

   Experiments were conducted at a temperature of 30-35 ºC, 10ppm ferric chloride as coagulant, 50% recycle ratio, pH 8, and 10 minutes treatment time  to find oil and grease (OG) and turbidity removal efficiencies at saturation pressure (2-6) bar.

ILs were used at concentration of 50 µl/liter of treated water in two positions in DAF system; the saturation vessel and the treatment tank. The performance using ILs

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Publication Date
Tue Jul 30 2019
Journal Name
Sn Applied Sciences
Removal of oil emulsion from aqueous solution by using Ricinus communis leaves as adsorbent
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Publication Date
Tue Jan 01 2013
Journal Name
International Journal Of Advances In Pharmacy, Biology And Chemistry
Synthesis of NSAID with Sulfonamide Conjugates as Possible Mutual Prodrugs using Amino Acid Spacer
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The purpose of this research work is to synthesize conjugates of NSAIDs (ibuprofen, and naproxen) with sulfadiazine as possible mutual prodrugs to overcome the local gastric irritation of NSAIDs with free carboxyl group by formation of ester linkage that supposed to remain intact in stomach and may hydrolyze in intestine chemically or enzymatically; in addition to that attempting to target the synthesized derivative to the colon by formation of azo bond that undergo reduction only by colonic bacterial azoreductaze enzyme to liberate the parent compound to act locally (treatment of inflammation and infections in colon)

Publication Date
Wed Dec 01 2010
Journal Name
Iraqi Journal Of Physics
Study of electron energy distribution function and transport parameters for CF4, Ar gases mixture discharge by using the solution of Boltzmann equation-Part II
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The Boltzmann transport equation is solved by using two- terms approximation for pure gases and mixtures. This method of solution is used to calculate the electron energy distribution function and electric transport parameters were evaluated in the range of E/N varying from . 172152110./510.VcmENVcm
The electron energy distribution function of CF4 gas is nearly Maxwellian at (1,2)Td, and when E/N increase the distribution function is non Maxwellian. Also, the mixtures are have different energy values depending on transport energy between electron and molecule through the collisions. Behavior of electrons transport parameters is nearly from the experimental results in references. The drift velocity of electron in carbon tetraflouride i

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Publication Date
Wed Dec 01 2010
Journal Name
Iraqi Journal Of Physics
Study of electron energy distribution function and transport parameters for CF4 and Ar gases discharge by using the solution of Boltzmann equation-Part I
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The Boltzmann transport equation is solved by using two- terms approximation for pure gases . This method of solution is used to calculate the electron energy distribution function and electric transport parameters were evaluated in the range of E/N varying from . 172152110./510.VcmENVcm
From the results we can conclude that the electron energy distribution function of CF4 gas is nearly Maxwellian at (1,2)Td, and when E/N increase the distribution function is non Maxwellian. Behavior of electrons transport parameters is nearly from the experimental results in references. The drift velocity of electron in carbon tetraflouride is large compared with other gases

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