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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
Thu Aug 01 2019
Journal Name
Transylvanian Review
POSSIBILITY OF APPLICATION THE BALANCED SCORECARD IN THE IRAQI INDUSTRIAL COMPANIES: A PROPOSED MODEL
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POSSIBILITY OF APPLICATION THE BALANCED SCORECARD IN THE IRAQI INDUSTRIAL COMPANIES: A PROPOSED MODEL

Publication Date
Tue Mar 02 2021
Journal Name
Humanitarian And Natural Sciences Journal
THE LINGUISTIC STRUCTURES OF THE HISTORIANS ALYAQOUBI (284 AH / 897 AD) ARE A MODEL
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The research in the linguistic structures of the historians Al-Yaqoubi is considered a model of the important topics in historical studies in general, given its importance in the lives of peoples due to its connotations and meanings that summarize interpretation, clarification, and prolonged speech, as it includes life meanings with many dimensions, these structures have been used in historical incidents Important, and throughout the different ages, as it can be used to support an opinion, solve problems, prove evidence, increase wisdom, and it needs rich life experiences, and a sound language, to use it, and needs a wide absorptive capacity for the recipient, the research included linguistic structures in the achievement of science , Lingu

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Publication Date
Mon Dec 30 2024
Journal Name
Wasit Journal For Pure Sciences
A New Class of Higher Derivatives for Harmonic Univalent Functions Established using a Generalized Fractional Integral Operator
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A new class of higher derivatives  for harmonic univalent functions defined by a generalized fractional integral operator inside an open unit disk E is the aim of this paper.

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Publication Date
Tue Sep 11 2018
Journal Name
Iraqi Journal Of Physics
Analytical study of high absorption region of the absorption edge of a-Si:H using nonlinear regression method
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This research is concerned with the re-analysis of optical data (the imaginary part of the dielectric function as a function of photon energy E) of a-Si:H films prepared by Jackson et al. and Ferlauto et al. through using nonlinear regression fitting we estimated the optical energy gap and the deviation from the Tauc model by considering the parameter of energy photon-dependence of the momentum matrix element of the p as a free parameter by assuming that density of states distribution to be a square root function. It is observed for films prepared by Jackson et al. that the value of the parameter p for the photon energy range is is close to the value assumed by the Cody model and the optical gap energy is which is also close to the value

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Publication Date
Sun Apr 03 2022
Journal Name
Iraqi Journal Of Laser
On the use of Aluminium as a plasmonic material in polarization rotators based on a hybrid plasmonic waveguide
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: The Aluminium (Al) material emerged as a plasmonic material in the wavelength ranges from the ultraviolet to the visible bands in different on-chip plasmonic applications. In this paper, we demonstrate the effect of using Al on the electromagnetic (EM) field distribution of a compact hybrid plasmonic waveguide (HPW) acting as a polarization rotator. We compare the performance of Al with other familiar metals that are widely used as plasmonic materials, which are Silver (Ag) and Gold (Au). Furthermore, we study the effect of reducing the geometrical dimensions of the used materials on the EM field distributions inside the HPW and, consequently, on the efficiency of the polarization rotation. We perform the study based o

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Publication Date
Wed Jan 01 2025
Journal Name
Aip Conference Proceedings
Comparative analysis of parameter estimation methods for Meixner process using wavelet packet transform
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The current research creates an overall relative analysis concerning the estimation of Meixner process parameters via the wavelet packet transform. Of noteworthy presentation relevance, it compares the moment method and the wavelet packet estimator for the four parameters of the Meixner process. In this paper, the research focuses on finding the best threshold value using the square root log and modified square root log methods with the wavelet packets in the presence of noise to enhance the efficiency and effectiveness of the denoising process for the financial asset market signal. In this regard, a simulation study compares the performance of moment estimation and wavelet packets for different sample sizes. The results show that wavelet p

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Publication Date
Tue Jun 27 2023
Journal Name
Journal Of Global Innovations In Agricultural Sciences
The use of remote sensing technology in defining the water depth in the lakes and water bodies: Western Iraq as a case study
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The study's primary purpose is to explore an appropriate way of monitoring and assessing water depths using the satellite remote sensing technique of the Al Habbaniyah Lake in Iraq. This research studied the experience-conditions (thresholds) of different bands for multi-temporal satellite image data with different satellite image sensors (Landsat 5-TM, and EO1-ALI) for the same region, to recognize regions of water depths. The threshold values are taken that to separate the Al Habbaniyah Lake to the required depths (shallow, deep, and very deep), as a supervised method. A three-dimension feature space plot had used to represent these regions. The relationship of the mean values of the three separated water regions with all TM and A

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Publication Date
Thu Dec 01 2022
Journal Name
Al-khwarizmi Engineering Journa
Comparative Study between Activated Carbon and Charcoal for the Development of Latent Fingerprints on Nonporous Surfaces
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For criminal investigations, fingerprints remain the most reliable form of personal identification despite developments in other fields like DNA profiling. The objective of this work is to compare the performance of both commercial charcoal and activated carbon powder derived from the Alhagi plant to reveal latent fingerprints from different non-porous surfaces (cardboard, plain glass, aluminum foil sheet, China Dish, Plastic, and Switch). The effect of three variables on activated carbon production was investigated. These variables were the impregnation ratio (the weight ratio of KOH: dried raw material), the activation temperature, and the activation time. The effect factors were investigated using Central Composite Design (CCD) softwa

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Publication Date
Thu Dec 01 2022
Journal Name
Al-khwarizmi Engineering Journal
Comparative Study between Activated Carbon and Charcoal for the Development of Latent Fingerprints on Nonporous Surfaces
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For criminal investigations, fingerprints remain the most reliable form of personal identification despite developments in other fields like DNA profiling. The objective of this work is to compare the performance of both commercial charcoal and activated carbon powder derived from the Alhagi plant to reveal latent fingerprints from different non-porous surfaces (cardboard, plain glass, aluminum foil sheet, China Dish, Plastic, and Switch). The effect of three variables on activated carbon production was investigated. These variables were the impregnation ratio (the weight ratio of KOH: dried raw material), the activation temperature, and the activation time. The effect factors were investigated using Central Composite Design

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Publication Date
Tue Nov 01 2022
Journal Name
Journal Of Engineering
Comparative Study on the Hardness of Mechroha Water Springs
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The vacancy of natural resources is undoubtedly limited by time. The sustainable development principle recommends modern technology for its protection and renewal. This project conducted analyses on two underground water sources in the north of Algeria (Mechroha Province). Besides, the use of the hardness factor and the adoption of the titration method, which is  the determining the concentration of an unknown solution using a known solution concentration, have permitted the characterization of the examples taken and to verify their conformity to the standard required, the results found showed HT=6.66 French degrees (oF) ) for Ain Guilloume water spring in comparison to Ain Messai water spring H

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