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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 Jan 01 2024
Journal Name
Journal Of Stomatology
The effect of Winter’s red line, angle of impaction, and radio-morphometric indices on surgical difficulty of impacted mandibular third molar: a prospective observational study
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Publication Date
Fri Jul 23 2021
Journal Name
International Journal Of Nonlinear Analysis And Applications
On the dynamical behavior of an eco-epidemiological model
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The aim of this article is to study the dynamical behavior of an eco-epidemiological model. A prey-predator model comprising infectious disease in prey species and stage structure in predator species is suggested and studied. Presumed that the prey species growing logistically in the absence of predator and the ferocity process happened by Lotka-Volterra functional response. The existence, uniqueness, and boundedness of the solution of the model are investigated. The stability constraints of all equilibrium points are determined. The constraints of persistence of the model are established. The local bifurcation near every equilibrium point is analyzed. The global dynamics of the model are investigated numerically and confronted with the obt

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Publication Date
Thu Dec 31 2020
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
STUDY THE SENSORY PROPERTIES OF SOME TYPES OF JUICES THAT MADE BY USING NATURAL SWEETENER POWDER (Stevia rebaudiana): STUDY THE SENSORY PROPERTIES OF SOME TYPES OF JUICES THAT MADE BY USING NATURAL SWEETENER POWDER (Stevia rebaudiana)
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Increased diseases and obesity currently due to increased production and excessive consumption of foods manufactured from non-food sweeteners without attention to the risk of consuming those additional high calories due to consuming these refreshing products such as juices and other various drinks, especially in the summer season by most segments of Iraqi society, especially workers, children and school students the aim of this study. Therefore, the study designed to replace sucrose with 0.03, 0.04 and 0.05% of each of the white stevia crystals and milled dry stevia leaves in the laboratory manufacture of juices and its effect on the general and sensory characteristics and the extent of their acceptability among the specialized r

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Publication Date
Sat Dec 15 2018
Journal Name
Journal Of Baghdad College Of Dentistry
Immunohistochemical expression of endocan, as a marker of assessment of angiogenic potential in benign vascular lesions (hemangioma, lymphangioma and lobular capillary hemangioma) of head and neck region
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 BACKGROUND: Vascular tumors are a heterogeneous group of diseases with biological behavior ranging from a hamartomatous growth to frank malignant. The pathophysiology of lymphangioma, vascular malformation and hemangioma is interconnected, blood vessels known to be the site of origin of hamartomas, venous malformations and some neoplasms as benign, tumor-like growth of vessels (hemangiomas). Angiogenesis is the process of formation of new blood vessels from an existing structure.

Aims of study Assessment of angiogenic potential in benign vascular lesions (hemangioma, lymphangioma and lobular capillary hemangioma) of head and neck region.

 Materials and Methods: Twenty-two formalin-fixed paraffin-embedd

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Publication Date
Sun Sep 01 2013
Journal Name
2013 Ieee International Conference On Circuits And Systems (iccas)
Improved undetected error probability model for JTEC and JTEC-SQED coding schemes
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The undetected error probability is an important measure to assess the communication reliability provided by any error coding scheme. Two error coding schemes namely, Joint crosstalk avoidance and Triple Error Correction (JTEC) and JTEC with Simultaneous Quadruple Error Detection (JTEC-SQED), provide both crosstalk reduction and multi-bit error correction/detection features. The available undetected error probability model yields an upper bound value which does not give accurate estimation on the reliability provided. This paper presents an improved mathematical model to estimate the undetected error probability of these two joint coding schemes. According to the decoding algorithm the errors are classified into patterns and their decoding

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Publication Date
Thu Jan 01 2015
Journal Name
Aip Conference Proceedings
Numerical solution for weight reduction model due to health campaigns in Spain
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This paper introduces a non-conventional approach with multi-dimensional random sampling to solve a cocaine abuse model with statistical probability. The mean Latin hypercube finite difference (MLHFD) method is proposed for the first time via hybrid integration of the classical numerical finite difference (FD) formula with Latin hypercube sampling (LHS) technique to create a random distribution for the model parameters which are dependent on time t . The LHS technique gives advantage to MLHFD method to produce fast variation of the parameters’ values via number of multidimensional simulations (100, 1000 and 5000). The generated Latin hypercube sample which is random or non-deterministic in nature is further integrated with the FD method t

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Publication Date
Wed Jul 01 2020
Journal Name
Journal Of Engineering
Bat Algorithm Based an Adaptive PID Controller Design for Buck Converter Model
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The aim of this paper is to design a PID controller based on an on-line tuning bat optimization algorithm for the step-down DC/DC buck converter system which is used in the battery operation of the mobile applications. In this paper, the bat optimization algorithm has been utilized to obtain the optimal parameters of the PID controller as a simple and fast on-line tuning technique to get the best control action for the system. The simulation results using (Matlab Package) show the robustness and the effectiveness of the proposed control system in terms of obtaining a suitable voltage control action as a smooth and unsaturated state of the buck converter input voltage of ( ) volt that will stabilize the buck converter sys

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Publication Date
Mon May 04 2020
Journal Name
Offshore Technology Conference
Hydrate Equilibrium Model for Gas Mixtures Containing Methane, Nitrogen and Carbon Dioxide
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Abstract<p>Gas hydrate formation is considered one of the major problems facing the oil and gas industry as it poses a significant threat to the production, transportation and processing of natural gas. These solid structures can nucleate and agglomerate gradually so that a large cluster of hydrate is formed, which can clog flow lines, chokes, valves, and other production facilities. Thus, an accurate predictive model is necessary for designing natural gas production systems at safe operating conditions and mitigating the issues induced by the formation of hydrates. In this context, a thermodynamic model for gas hydrate equilibrium conditions and cage occupancies of N2 + CH4 and N2 + CO4 gas mix</p> ... Show More
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Publication Date
Thu Nov 17 2022
Journal Name
Journal Of Information And Optimization Sciences
Hybrid deep learning model for Arabic text classification based on mutual information
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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The impact of financing structure on bank profits : Applied research on a sample of commercial banks listed in the Iraq Stock Exchange for the period (2011-2020)
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The research aims to identify the concept of financing structure and what are the determinants that affect it and the goals achieved by financing in commercial banks in addition to the sources upon which the financing structure depends consisting of internal financing sources and external financing sources and their connection to the profits of commercial banks. Baghdad, Khaleeji Commercial Bank) registered in the Iraq Stock Exchange during the period for the years (2011-2020) published in the Iraq Stock Exchange from and the research relied on financial analysis tools to analyze the independent variable the following financing structure (the ratio of equity to total assets, the ratio of deposits to Total liabilities, the ratio of loans

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