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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 Apr 02 2019
Journal Name
Artificial Intelligence Research
A three-stage learning algorithm for deep multilayer perceptron with effective weight initialisation based on sparse auto-encoder
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A three-stage learning algorithm for deep multilayer perceptron (DMLP) with effective weight initialisation based on sparse auto-encoder is proposed in this paper, which aims to overcome difficulties in training deep neural networks with limited training data in high-dimensional feature space. At the first stage, unsupervised learning is adopted using sparse auto-encoder to obtain the initial weights of the feature extraction layers of the DMLP. At the second stage, error back-propagation is used to train the DMLP by fixing the weights obtained at the first stage for its feature extraction layers. At the third stage, all the weights of the DMLP obtained at the second stage are refined by error back-propagation. Network structures an

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Publication Date
Wed Sep 15 2021
Journal Name
Al-academy
The plastic structure in the lyrical introduction to pre-Islamic poetry " The hanging Tarfa bin Al-Abd as a model": زينب خليل حسين
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The research deals with the lyrical introduction in the commentary of Tarfa bin al-Abd as a formative system characterized by flexibility and richness of imagination, which achieved a formative treatment and a unique construction within the structures of the structural and semantic language. I dealt with the poetic verses represented by the lyrical introduction as a formative hypothesis, basing its goal on a methodological framework distributed on the problem that was summarized by the following question: Is it possible to look at the poetic pattern within the pre-Islamic poem / hanging blinking as a model, in its plastic dimensions and to identify the stylistic treatment that achieves the formation space within the poetic text. The rese

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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
The Effect of Artificial Accelerated Aging on The Color of Ceramic Veneers Cemented With Different Resin Cements (A Comparative In Vitro Study)
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ABSTRACT Background: Color changes that are detectable to human eye can affect the esthetic appearance of ceramic veneers. The purpose of this study was to evaluate and compare the effect of artificial accelerated aging on the color of ceramic veneers cemented with different resin cements. Materials and Methods: Sixty discs were prepared with 0.5 mm thickness, 30 discs made from IPS e.max press (Ivoclar Vivadent) and 30 discs were made from VITA Enamic (VITA Zahnfabrik). The discs were cemented with three resin cements: Variolink Veneer MV 0 shade (Ivoclar Vivadent), Rely X veneer Translucent shade (3M ESPE) and NX3 Nexus Clear shade (Kerr Corporation) with 0.1 mm thickness. The spectrophotometer Easyshade Advance was used to measure the co

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Publication Date
Thu Oct 01 2009
Journal Name
Jssdds
Topical 10% lactic acid solution in the treatment of pityriasis versicolor in comparison with topical 1% clotrimazol solution (single-blind, comparative and therapeutic study)
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KE Sharquie, AA Noaimi, AM Oweid, JSSDDS, 2009 - Cited by 2

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Publication Date
Sun Jan 01 2017
Journal Name
Dissertation/thesis
A Model To Evaluate the Online Training for Global Virtual Teams in Global Software Projects
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Publication Date
Thu Jan 01 2026
Journal Name
Iraqi Journal Of Science
Magnetohydrodynyamic Flow for a Viscoclastic Fluid with the Generalized Oldroyd-B Model with Fractional Derivative
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This paper deals with the Magnetohydrodynyamic (Mill)) flow for a viscoclastic fluid of the generalized Oldroyd-B model. The fractional calculus approach is used to establish the constitutive relationship of the non-Newtonian fluid model. Exact analytic solutions for the velocity and shear stress fields in terms of the Fox H-function are obtained by using discrete Laplace transform. The effect of different parameter that controlled the motion and shear stress equations are studied through plotting using the MATHEMATICA-8 software.

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Publication Date
Sun Sep 07 2014
Journal Name
Baghdad Science Journal
Optimum conditions for ascorbic acid determination in three Iraqi citrus using HPLC technique
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A high-performance liquid chromatography method was employed for the quantitative determination of ascorbic acid (AA) which called vitamin C in three types of Iraqi citrus (orange mandarin and aurantium ) and to establish this goal , evaluation of ascorbic acid degradation is so important due to its significant criticality when exposure to ordinary atmospheric conditions. The chromatographic analysis of AA was carried out after their sequential elution with KH2PO4 ( as mobile phase) by reverse-phase HPLC technique with C8 column and UV detection at 214 nm. .Bad resolutions was appeared clearly for C8 column , so another alternative condition were carried out to improve the resolution by replacement of C8 by C18 column .Statistical treat

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of Global Pharma Technology
Nanocrystal Technology as a Tool for Improving Dissolution of Poorly Soluble Drugs
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Many approaches have been developed over time to counter the bioavailability limitations of poorly soluble drugs. With advances in nanotechnology in recent decades, this issue has been approached through the formulation of drugs as nanocrystals. Nanocrystals consist of pure drug(s) and a minimum of surface active agent(s) required for stabilization. They are carrier-free submicron colloidal drug delivery systems with a mean particle size typically in the range of 200 - 500 nm. By reducing particle size to nanoscale, the surface area available for dissolution is increased, and thus bioavailability is enhanced. Drug nanocrystals constitute a versatile formulation approach to enhance the pharmacokinetic and pharmacodynamic properties of poorly

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Publication Date
Tue Mar 01 2016
Journal Name
Journal Of Engineering
Critical Success Factors in Construction Projects (Governmental Projects as a Case Study)
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The importance of the construction sector and its Great role in the provision of services and infrastructure, reduce poverty, improve living conditions and improve the economic situation in the country, impose attention to the way in which the projects implemented for its improvement and to get successful projects. The objective of this research was to determine the criteria for success as well as critical success and failure factors that have a significant impact on project success. A selected 75 engineer (department managers, project managers and engineers) are asked to fill  the questionnaire form, Sixty-seven valid questionnaire forms were analyzed statistically to get search results, which were as follows : Twe

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Publication Date
Mon May 12 2025
Journal Name
The International Journal Of The History Of Sport
Exploring Sport’s Role in Mitigating Conflicts Gulf Cup as a Case Study
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Conflict, peace, and sports have a long history as practical realities, and their correlation has become an important subject of study in the last decades of the twentieth century. Sport has infiltrated peace and conflict studies as a tool for resolving conflict and building peace, but opinions have differed between those who say it is a positive tool and others who see it as negative. The Gulf Cup is one of the champions that have never been studied, and in-depth research about it has not been done. This tournament has affected the relations between the states involved. The politics cast its shadow on the Gulf Cup. The paper aims to shed light on how political events in the region have consistently affected the Gulf Cup and how politics in

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