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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 Oct 25 2022
Journal Name
Chalcogenide Letters
Study the properties of Cu2Se thin films for optoelectronic applications
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Copper selenide (Cu2Se) thin films were prepared by thermal evaporation at RT with thickness 500 nm. The heat-treating for (400 &500) K for the absorber layer has been investigated. This research includes, studying the structural properties of X-ray diffraction (XRD) that show the Cu2Se thin film (Cubic) and has a polycrystalline orientation prevalent (220). Moreover, studying the effect of annealing on their surface morphology properties by using Atomic Force Microscopy AFM. Optical properties were considered using the transmittance and absorbance spectra had been recorded when wavelength range (400 - 1000) nm in order to study the absorption coefficient and energy gap. It was found that these films had allowed direct transitio

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Publication Date
Wed Feb 20 2019
Journal Name
Iraqi Journal Of Physics
Study the atomic properties of 2s shell for some atoms
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Ground state energies and other properties of 2S shell for some atoms as Be(Z=4), B(Z=5), C(Z=6) and N(Z=7) were calculated by using Hartree-Fock wave function. We found the values of potential energies in hartree unit (3.8369, 6.78565, 10.18852 and 14.41089) respectively and the other proprieties like expectation values of the position < r1m >  were in agreement with the published results. All the studied atomic properties were normalized. 

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Publication Date
Fri Mar 01 2024
Journal Name
Medicine Advances
Quality of life, adherence and knowledge of epileptic patients and the impact of a pharmacist‐led educational intervention: A review
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Around 65 million individuals suffer from epilepsy worldwide, and when it is not properly treated, it is linked to higher rates of physical harm and mortality. Due to the requirement for long‐term therapy and the side effects of many medications, medication compliance is a significant issue. The purpose of this review was to summarize the findings of previous studies examining the quality of life (QOL), adherence, patient education, and medication knowledge, as well as the impact of a pharmacist‐led educational intervention. Additionally, to find out if these studies benefit epileptic patients, to find the appropriate method used to help them in all aspects of their lives, and to use these in future studies. A systematic and comprehensi

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Publication Date
Tue Nov 29 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A proposed form for the Combined Assurance report and its impact In achieving sustainable development in the Iraqi economic units
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Despite the importance of sustainable development and its dimensions in developing performance and supporting competitive advantage in economic units, there is a gap and lack of coordination between Combined Assurance  providers (management, internal audit, external audit) to report on sustainable development, and the research aims to propose a model for the Combined Assurance report to achieve development sustainable development in the Iraqi economic units, especially the Baghdad Municipality, enables assurance providers to coordinate efforts that lead to the achievement of Combined Assurance, The research found the proposed model for the Combined Assurance report in achieving sustainable development in the Iraqi economic units, es

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Publication Date
Sat Sep 30 2017
Journal Name
Al-khwarizmi Engineering Journal
A Cognitive Hybrid Tuning Control Algorithm Design for Nonlinear Path-Tracking Controller for Wheeled Mobile Robot
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Abstract

This research presents a on-line cognitive tuning control algorithm for the nonlinear controller of path-tracking for dynamic wheeled mobile robot to stabilize and follow a continuous reference path with minimum tracking pose error. The goal of the proposed structure of a hybrid (Bees-PSO) algorithm is to find and tune the values of the control gains of the nonlinear (neural and back-stepping method) controllers as a simple on-line with fast tuning techniques in order to obtain the best torques actions of the wheels for the cart mobile robot from the proposed two controllers. Simulation results (Matlab Package 2012a) show that the nonlinear neural controller with hybrid Bees-PSO cognitive algorithm is m

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Publication Date
Tue Oct 01 2024
Journal Name
Journal Of Engineering
A Comprehensive Review for Integrating Petrophysical Properties, Rock Typing, and Geological Modeling for Enhanced Reservoir Characterization
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Reservoir characterization is an important component of hydrocarbon exploration and production, which requires the integration of different disciplines for accurate subsurface modeling. This comprehensive research paper delves into the complex interplay of rock materials, rock formation techniques, and geological modeling techniques for improving reservoir quality. The research plays an important role dominated by petrophysical factors such as porosity, shale volume, water content, and permeability—as important indicators of reservoir properties, fluid behavior, and hydrocarbon potential. It examines various rock cataloging techniques, focusing on rock aggregation techniques and self-organizing maps (SOMs) to identify specific and

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Investigation of density and form factor of some F isotopes using Hartree-Fock and shell model calculations
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Structure of unstable 21,23,25,26F nuclei have been investigated
using Hartree – Fock (HF) and shell model calculations. The ground
state proton, neutron and matter density distributions, root mean
square (rms) radii and neutron skin thickness of these isotopes are
studied. Shell model calculations are performed using SDBA
interaction. In HF method the selected effective nuclear interactions,
namely the Skyrme parameterizations SLy4, Skeσ, SkBsk9 and
Skxs25 are used. Also, the elastic electron scattering form factors of
these isotopes are studied. The calculated form factors in HF
calculations show many diffraction minima in contrary to shell
model, which predicts less diffraction minima. The long tail

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The role of the green human resources management practices in a achieving requirements of environmental citizenship- Field research at the General Company for Vegetable Oils.
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The research aims to determine the role of the practices of green human resources management in achieving requirements of environmental citizenship in the workplace, the General Company for Vegetable Oils was chosen for the application of field-side of research which represent one of the important industrial companies in Iraq, which suffers from poor Green human resources management applications, which reflected negatively on the development Environmental citizenship among Employees. The questionnaire use as a tool to collect data and information as well as field presence of the researcher, The research sample included (30) managers of departments and Division ,and through using statistical program (SPSS) the data has been analys

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Publication Date
Wed Feb 03 2016
Journal Name
Iraqi Journal Of Physics
Study the variation of synodic month for the moon through 2000-2100
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In this research study the synodic month for the moon and theirrelationship with the mean anomaly for the moon orbit and date A.Dand for long periods of time (100 years), we was design a computerprogram that calculates the period of synodic months, and thecoordinates of the moon at the moment of the new moon with highaccuracy. During the 100 year, there are 1236 period of synodicmonths.We found that the when New Moon occurs near perigee (meananomaly = 0°), the length of the synodic month at a minimum.Similarly, when New Moon occurs near apogee (mean anomaly =180°), the length of the synodic month reaches a maximum. Theshortest synodic month on 2053 /1/ 16 and lasted (29.27436) days.The longest synodic month began on 2008 /11/ 27 a

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Publication Date
Sun Feb 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
An analytical study at the General Company for the manufacture of batteries
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    This study carry’s out the correlation and the effect of two main variables, these variables are Job Satisfaction included six sub: wages - salaries and justice and yield, working  conditions    and services, pattern of supervision and the relationship with the manger, Relationship with colleagues, the content of the work and the variety of tasks, development and  promotion  opportunities available  to  an individual,   and Organizational Performance included  two sub variables:  Efficiency, Effectiveness.  This research was conducted using a questioner as a main tool, This questioner was distributed randomly to a research community composed of

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