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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
Mon Feb 18 2019
Journal Name
Iraqi Journal Of Physics
STVI calculating the changes in vegetable cover for a vegetated environment in west Iraq
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Remote sensing provide the best means to monitoring change in vegetation over a wide range of temporal scales over large areas. In this study, the vegetation index which has been applied known as the Stress Related Vegetation Index (STVI) on in the area around the Euphrates River and part of Al-Habbaniyah lake which located at western side of the river in Ramadi city, Al-Anbar province at Iraq to study the vegetation cover changes and detect the areas of changes, using two satellite sensors multispectral images such as TM and ALI, after geometric correction procedure to rectifying these images. The STVI-4 index result was the best than other vegetation indices (STVI-1 and STVI-3) to discriminate the vegetable cover distribution. The diff

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Publication Date
Fri Mar 01 2024
Journal Name
Partial Differential Equations In Applied Mathematics
A hybrid technique for solving fractional delay variational problems by the shifted Legendre polynomials
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This study presents a practical method for solving fractional order delay variational problems. The fractional derivative is given in the Caputo sense. The suggested approach is based on the Laplace transform and the shifted Legendre polynomials by approximating the candidate function by the shifted Legendre series with unknown coefficients yet to be determined. The proposed method converts the fractional order delay variational problem into a set of (n + 1) algebraic equations, where the solution to the resultant equation provides us the unknown coefficients of the terminated series that have been utilized to approximate the solution to the considered variational problem. Illustrative examples are given to show that the recommended appro

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Publication Date
Sun Dec 01 2013
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The application target cost technique by using reverse engineering: An application study in the general company for vegetable oils industry
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The Purpose of this study is mainly to improve the competitive position of products economic units using technique target cost and method reverse engineering and through the application of technique and style on one of the public sector companies (general company for vegetable oils) which are important in the detection of prices accepted in the market for items similar products and processing the problem of high cost which attract managerial and technical leadership to the weakness that need to be improved through the introduction of new innovative solutions which make appropriate change to satisfy the needs of consumers in a cheaper way to affect the decisions of private customer to buy , especially of purchase private economic units to

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Publication Date
Sun Sep 02 2012
Journal Name
Baghdad Science Journal
Determination of optimal conditions for laccase production by Pleurotus ostreatus using sawdust as solid medium and its use in phenol degradation
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The ability of four local fungal isolates for extracellular laccase production has been tested with five grams 1:1(w/v) humidified sawdust as substrate in mineral salt medium. After 21 day of incubation at 25±1 ? C and using one mycelial plug (5mm), higher level of laccase activity (0.15U/ml) and specific activity (15U/mg) were observed by Pleurotus ostreatus in comparison with other fungal isolates. The results of optimum conditions for laccase production from selected isolate showed that, the maximum laccase activity (0.55U/ml) and specific activity (55U/mg) were obtained at moisture ratio 1:3 (w/v), using 3 mycelial plugs (5 mm), after 15 days incubation period at 25±1 ? C. The results of phenol degradation by crud laccase revealed th

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Synthesis, Characterization and Textural Analysis of Functionalized Mesoporous Silica Using Sodium Silicate as Precursor and Silicone Surfactant as Template
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Three mesoporous silica with different functional group were prepared by one-step synthesis based on the simultaneous hydrolysis and condensation of sodium silicate with organo - silane in the presence of template surfactant polydimethylsiloxane - polyethyleneoxide (PDMS - PEO). The prepared materials were characterized by Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), atomic force microscopy (AFM) and nitrogen adsorption/desorption experiments. The results indicate that the preparation of methyl and phenyl functionalized silica were successful and the mass of methyl and phenyl groups bonded to the silica structure are 15, 38 mmol per gram silica. The average diameter of the silica particles are 103.51,

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Publication Date
Thu Oct 18 2018
Journal Name
European Journal Of Organic Chemistry
PdII-Mediated Oxidative Amination for Access to a 9-Azabicyclo[4.2.1]nonane Compound Library and Anatoxin-a
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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The effect of the Banking Capital on Finance Fixed Assets of the Bank: An Applied Study on a Sample of Iraqi Private Banks
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To the Banks capital several uses, including the protection of deposits and this was approved by the Basel Committee, And Finance long-term investments which intended to investment in fixed assets that are essential to the continuation of banking activity, Fixed assets not financed from the funds of the deposit, but the owner equity do this jop. the current research tries to prove the effect of banks capital on fixed assets for a sample of iraqi private banks (bank of baghdad and Iraqi middle east Investment bank), for the period from 2011 until 2014. The research concluded that the capital of bank of baghdad affect on his total fixed assets by (84%), and the capital of Iraqi middle east Investment bank affect on his total fixed assets b

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Publication Date
Tue Dec 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Building a strategic perspective on the system of governance and measuring the level of its performance Survey study at the University of Basra
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The Local and Global Corporations are suffering of managerial and financial corruption phenomena, which leads them to loss and bankruptcy. So, it is necessary to search for tools which help prevent phenomena like this, and one of these tools is (corporate governance) which represent controlling tool that contribute in reducing corruption. this study aims at modifying (corporate governance system)in order to make it suitable with Iraqi government Corporations. the study depend upon main hypothesis which is (the performance level of the strategic perspective of governance system is depending upon work according to the perspective dimensions itself.  From the main conclusions:-It is possible to building a strategic perspective

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Publication Date
Mon Apr 03 2023
Journal Name
Journal Of Educational And Psychological Researches
Attitudes of the Private Sector towards the Application of Operational Contracting in Private Education Schools in the Sultanate of Oman: A Qualitative Study
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Abstract

The research aims to investigate the private sector attitudes toward operational contracting in special education schools. The research adopted the qualitative approach by using personal interviews with a sample of (45) private school owners and managers in Oman. The results of the research revealed that there is an agreement among the majority of respondents on the ability of the private sector to manage special education schools, the advantages of the partnership, as well as the need for guarantees to support this partnership. The government should fully assume it. The role of the private sector remains to raise the operational efficiency of schools. Opinions vary about the level of powers granted to t

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Publication Date
Wed Mar 01 2023
Journal Name
Iraqi Journal Of Physics
Design and Construction of a Dust Detection System using Infrared Laser: The Case of Dust Storms in Baghdad in the Summer 2022
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Iraq suffers from serious pollution with harmful particles that have important direct and indirect effects on human activities and human health. In this research, a system for detecting pollutants in the air was designed and manufactured using infrared laser technology. This system was used to detect the presence of pollutants in the dust storms that swept the city of Baghdad which could have a negative impact on human health and living organisms.

The designed detection system based on the use of infrared laser (IR) with a wavelength of 1064 nm was used for the purposes of detecting pollutants based on the scattering of the laser beam from these pollutants. The system was aligned to obtain the best signal for the scattered rays, w

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