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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
Wed Jun 12 2013
Journal Name
International Journal Of Computer Applications
Design and Implementation of a Practical FTTH Network
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Fiber-to-the-Home (FTTH) has long been recognized as a technology that provides future proof bandwidth [1], but has generally been too expensive to implement on a wide scale. However, reductions in the cost of electro-optic components and improvements in the handling of fiber optics now make FTTH a cost effective solution in many situations. The transition to FTTH in the access network is also a benefit for both consumers and service providers because it opens up the near limitless capacity of the core long-haul network to the local user. In this paper individual passive optical components, transceivers, and fibers has been put together to form a complete FTTH network. Then the implementation of the under construction Baghdad/Al

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Publication Date
Wed May 31 2023
Journal Name
Iraqi Geological Journal
A Survey of Infill Well Location Optimization Techniques
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The maximization of the net present value of the investment in oil field improvements is greatly aided by the optimization of well location, which plays a significant role in the production of oil. However, using of optimization methods in well placement developments is exceedingly difficult since the well placement optimization scenario involves a large number of choice variables, objective functions, and restrictions. In addition, a wide variety of computational approaches, both traditional and unconventional, have been applied in order to maximize the efficiency of well installation operations. This research demonstrates how optimization approaches used in well placement have progressed since the last time they were examined. Fol

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Publication Date
Thu Nov 01 2001
Journal Name
Renewable Energy
Optoelectronic properties of a-Si1−xGex:H thin films
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Publication Date
Tue Dec 09 2014
Journal Name
Journal Of The College Of Education For Women
A Stylistic Analysis of Bisson’s Bears Discover Fire
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This paper aims at analyzing Terry Bisson’s short story Bears Discover Fire stylistically by following both Gerard Genette’s theory of narratology (1980) and Short and Leech (1981) strategy for analyzing fictional works. Also trying to examine to what extent these models are applicable in analyzing the selected story. Stylistic analysis procedures help the readers/researchers to identify specific linguistic features in order to support literary interpretation and appreciation of literary texts. Style in fiction concentrates not on what is written, but on how a text is written. Each writer has his own style and techniques which distinguish him from other writers

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Publication Date
Wed Dec 01 2021
Journal Name
Journal Of Biotechnology Research Center
Candida and Candidiasis - A review of Virulence Factors
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   The occurrences of invasive candidiasis has increased over the previous few decades. Although Candida albicans considers as one of the most common species of organisms, that cause acquired fungal infections. Candida albicans is an opportunistic fungal pathogen and inherent in as a lifelong, the yeast is present in healthy individuals as a commensal, and can reside harmlessly in human body. However, in immuno-compromised individuals, the fungus can invade tissues, producing superficial infections and, in severe cases, life-threatening systemic infections. This review wills emphasis on virulence factor of C. albicans including (adhesion, invasion, candida proteinase, and phenotypic switching and biofilm formation. I

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Publication Date
Sun Jan 01 2023
Journal Name
Route Educational And Social Science Journal
A POSTMODERNIST READING OF KURT VONNEGUT’S SLAUGHTERHOUSE-FIVE
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Publication Date
Sun Apr 01 2018
Journal Name
Journal Of Educational And Psychological Researches
EMDR impact on a sample of Displaced persons
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Abstract [email protected] Background: Acute Traumatic Stress Disorder (ATSD) might be complicated by Post Traumatic Stress Disorder (PTSD). Psychological First Aid (PFA) said to be helpful to reduce the possibility of reduction of ASD and PTSD symptoms. PFA is simple procedure to deliver help & support to victims, may be by some one close to him, quietly and professionally. Iraq has and is still experiencing, continuous traumatic stresses. ATSD is especially seen in war such as during the Gulf War, Embargo and nowadays under the current American occupation. With the extreme shortage of recourses and the given late priority to psychological problems and intervention have disastrous consequences on the psycho-social wellbeing of peop

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Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Cost of human resources from a behavioral perspective
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Purpose/objective:

1 - To explain the financial impact of the activities and areas of human resources management and the adoption of the methodology for estimating costs on the basis of conduct and statement of how to assess costs and benefits of human resource activities.

2 - Measuring  human capital, and its impact on the financial statements.

 

Design/methodology/approach:

 Concentrated dimensions of the research paper's lack of financial statements prepared by the organizations for information mandated human resource its components of the three (attraction - development

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Publication Date
Sat Oct 01 2011
Journal Name
Iraqi Journal Of Physics
Preparation of nano-microfibers with a different polymers
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Abstract: In this research, nanofibers have been prepared by using an electrospinning method. Three types of polymer (PVA, VC, PMMA) have been used with different concentration. The applied voltage and the gap length were changed. It was observed that VC is the best polymer than the other types of polymers.

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Publication Date
Fri Jan 01 2021
Journal Name
Int. J. Nonlinear Anal. Appl.
Analysis of a harvested discrete-time biological models
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This work aims to analyze a three-dimensional discrete-time biological system, a prey-predator model with a constant harvesting amount. The stage structure lies in the predator species. This analysis is done by finding all possible equilibria and investigating their stability. In order to get an optimal harvesting strategy, we suppose that harvesting is to be a non-constant rate. Finally, numerical simulations are given to confirm the outcome of mathematical analysis.

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