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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 Dec 01 2015
Journal Name
Journal Of Al-nahrain University-science
Synthesis of Polyacrylamides from Derivatives 2-Aminobenzothiazole and also Preparation of Dibutylphthalate as a Plasticizer to Estimate Plasticization Behaviour for Prepared Polymers
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Publication Date
Sat Aug 01 2020
Journal Name
Jordan Journal Of Physics
Theoretical Simulation of Backscattering Electron Coefficient for SixGe1-x/Si Heterostructure as a Function of Primary Electron Beam Energy and Ge Concentration
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Abstract: This study aims to investigate the backscattering electron coefficient for SixGe1-x/Si heterostructure sample as a function of primary electron beam energy (0.25-20 keV) and Ge concentration in the alloy. The results obtained have several characteristics that are as follows: the first one is that the intensity of the backscattered signal above the alloy is mainly related to the average atomic number of the SixGe1-x alloy. The second feature is that the backscattering electron coefficient line scan shows a constant value above each layer at low primary electron energies below 5 keV. However, at 5 keV and above, a peak and a dip appeared on the line scan above Si-Ge alloy and Si, respectively, close to the interfacing line

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A proposed model program to audit the contribution of municipal institutions to achieving the environmental dimension of sustainable development "applied research"
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Abstract

               The research aimed to prepare an audit program focusing on the activities of municipal institutions related to the environmental dimension as one of the dimensions of sustainable development, and applying the program for the purpose of preparing an oversight report related to assessing the impact of the activities of municipal institutions on the environmental reality as the main channel through which municipal institutions contribute to achieving the part related to it. Among the requirements of sustainable development, the proposed program was prepared and applied to the institutions affiliated to the Directorate of Mu

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Publication Date
Tue Mar 01 2016
Journal Name
Al-academy
Harmonization formative in the design of interior spaces Hall of discussions in the design department (a model): بدريا محمد حسن فرج
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Can not reach a comprehensive concept for interior design through the use of Harmonization term according transformations experienced by the terms of the variables associated with the backlog of cultures that characterize concepts according to the nature of the users of the spaces in the design output, which necessitates the meaning of the combination of knowledge, art, science, such as the type of perceptions design the Harmonization cognitive science with art to create products of the use of design configurations that help the designer to put such a product within the reality and like the fact that reliable, as well as the rational knowledge tend somehow to the objective specifically in facilitating the substance subject to perceptible

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Publication Date
Wed Mar 09 2022
Journal Name
Journal Of Craniofacial Surgery
The Use of Osseodensification for Ridge Expansion and Dental Implant Placement in Narrow Alveolar Ridges: A Prospective Observational Clinical Study
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The osseodensification (OD) drilling technique was suggested as an alveolar ridge expansion technique, so the aim of this prospective clinical study was to evaluate the amount of bone expansion obtained by the OD drilling technique and its effect on implant stability in patients with narrow alveolar ridges. The width of the alveolar ridge was measured at the crest before and after implant site preparation, whereas the implant stability was measured using Osstell Beacon implant stability quotient (ISQ). The ISQ values were recorded immediately postoperatively and after 16 weeks. Twenty-three patients were included; they received 40 implants. The mean (± standard deviation [SD]) amount of expansion was 1.29 (± 0.41) mm, and the difference b

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Publication Date
Sun Dec 01 2024
Journal Name
Journal Of Economics And Administrative Sciences
Nadaraya-Watson Estimation of a Circular Regression Model on Peak Systolic Blood Pressure Data
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Purpose: The research aims to estimate models representing phenomena that follow the logic of circular (angular) data, accounting for the 24-hour periodicity in measurement. Theoretical framework: The regression model is developed to account for the periodic nature of the circular scale, considering the periodicity in the dependent variable y, the explanatory variables x, or both. Design/methodology/approach: Two estimation methods were applied: a parametric model, represented by the Simple Circular Regression (SCR) model, and a nonparametric model, represented by the Nadaraya-Watson Circular Regression (NW) model. The analysis used real data from 50 patients at Al-Kindi Teaching Hospital in Baghdad. Findings: The Mean Circular Erro

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Publication Date
Mon Feb 01 2021
Journal Name
Iop Conference Series: Materials Science And Engineering
On modelling and adaptive control of a linear smart beam model interacting with fluid
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Abstract<p>This paper deals with modelling and control of Euler-Bernoulli smart beam interacting with a fluid medium. Several distributed piezo-patches (actuators and/or sensors) are bonded on the surface of the target beam. To model the vibrating beam properly, the effect of the piezo-patches and the hydrodynamic loads should be taken into account carefully. The partial differential equation PDE for the target oscillating beam is derived considering the piezo-actuators as input controls. Fluid forces are decomposed into two components: 1) hydrodynamic forces due to the beam oscillations, and 2) external (disturbance) hydrodynamic loads independent of beam motion. Then the PDE is discretized usi</p> ... Show More
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Publication Date
Sun Sep 01 2019
Journal Name
Baghdad Science Journal
An Analysis of a Partial Temporary Immunity SIR Epidemic Model with Nonlinear Treatment Rate
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     A partial temporary immunity SIR epidemic model involv nonlinear treatment rate is proposed and studied. The basic reproduction number  is determined. The local and global stability of all equilibria of the model are analyzed. The conditions for occurrence of local bifurcation in the proposed epidemic model are established. Finally, numerical simulation is used to confirm our obtained analytical results and specify the control set of parameters that affect the dynamics of the model.

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Publication Date
Mon Nov 06 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
Effect of hunting cooperation and fear in a food chain model with intraspecific competition
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Taking into account the significance of food chains in the environment, it demonstrates the interdependence of all living things and has economic implications for people. Hunting cooperation, fear, and intraspecific competition are all included in a food chain model that has been developed and researched. The study tries to comprehend how these elements affect the behavior of species along the food chain. We first examined the suggested model's solution properties before calculating every potential equilibrium point and examining the stability and bifurcation nearby. We have identified the factors that guarantee the global stability of the positive equilibrium point using the geometric approach. Additionally, the circumstances that would gu

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Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
A study of the solvent effect on the low temperature spectra of benzoanthracene molecules
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been taken at room temperature down to liquid nitrogen temperature (77K). Polar and nonpolar solvents have been used to study the solvent effect on the absorption and fluorescence spectra of solute molecules. Some of the spectroscopic parameters have been determined as functions of solvent polarity and temperature. The results indicate that the band width FWHM increases with increasing the solvent polarity and temperature, while the peak emission cross section decreases with increasing of solvent polarity and decreases with increasing the temperatures. Clear vibrational structure spectra of benzoanthracene molecules have been observed in Nonane and Hexane solvents at 77K.

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