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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 Apr 11 2024
Journal Name
Hemodialysis International
Using cryotherapy, <scp>EMLA</scp> (eutectic lidocaine/prilocaine) cream, or lidocaine spray to reduce pain during arteriovenous fistula puncture: A randomized controlled trial
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Abstract<sec><title>Introduction

In hemodialysis patients, pain associated with needle insertion into an arteriovenous fistula is a physical and psychological problem. The aim of this study was to assess the effectiveness of pre‐puncture application of an ice pack, EMLA cream, or lidocaine spray to reduce pain associated with access puncture.

Methods

This was a multicenter study done in nine hemodialysis centers in Iraq. The study utilized a randomized, parallel‐group design, in which patients being dialyzed using an arteriovenous access were allocated into one of four groups. Access puncture was preceded by nothing (contr

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Publication Date
Wed Aug 17 2022
Journal Name
Al–bahith Al–a'alami
Lawyers’ Use of the Website of the Supreme Judicial Council and the Gratifications Obtained from It Drawn Research Submitted for the Study of the Higher Professional Diploma
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The field study of this paper focused on the motives for lawyers to use the website
of the Supreme Judicial Council, and the gratifications achieved as a result of its use.
This study sought to achieve a number of goals, including:
1. Monitoring the patterns of lawyers’ use of the website of the Supreme Judicial Council.
2. Determining the forms that lawyers use to interact on the website of the Supreme
Judicial Council.
This study is a descriptive in kind as the researcher relied on the ‘survey method’ in
its study of the external audience (lawyers) using the questionnaire and scale toolThe questionnaire was distributed among a deliberately chosen sample, consisting of
(160) lawyers who used the website of

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Publication Date
Fri Mar 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Robust Two-Step Estimation and Approximation Local Polynomial Kernel For Time-Varying Coefficient Model With Balance Longitudinal Data
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      In this research, the nonparametric technique has been presented to estimate the time-varying coefficients functions for the longitudinal balanced data that characterized by observations obtained through (n) from the independent subjects, each one of them is measured repeatedly by group of  specific time points (m). Although the measurements are independent among the different subjects; they are mostly connected within each subject and the applied techniques is the Local Linear kernel LLPK technique. To avoid the problems of dimensionality, and thick computation, the two-steps method has been used to estimate the coefficients functions by using the two former technique. Since, the two-

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Random Number Generation for Quantum Key Distribution Systems Based on Shot-Noise Fluctuations in a P-I-N Photodiode
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A simple setup of random number generator is proposed. The random number generation is based on the shot-noise fluctuations in a p-i-n photodiode. These fluctuations that are defined as shot noise are based on a stationary random process whose statistical properties reflect Poisson statistics associated with photon streams. It has its origin in the quantum nature of light and it is related to vacuum fluctuations. Two photodiodes were used and their shot noise fluctuations were subtracted. The difference was applied to a comparator to obtain the random sequence.

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Publication Date
Wed Oct 25 2023
Journal Name
Journal Of Optics
Integrated gallium phosphide-waveguide polarization rotator based on rotating a horizontal slot by 45 degree for 700 nm wavelength
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Abstract<p>Polarization manipulation elements operating at visible wavelengths represent a critical component of quantum communication sub-systems, equivalent to their telecom wavelength counterparts. The method proposed involves rotating the optic axis of the polarized input light by an angle of 45 degree, thereby converting the fundamental transverse electric (TE<sub>0</sub>) mode to the fundamental transverse magnetic (TM<sub>0</sub>) mode. This paper outlines an integrated gallium phosphide-waveguide polarization rotator, which relies on the rotation of a horizontal slot by 45 degree at a wavelength of 700 nm. This will ultimately lead to the conception of a mode hybridization phenomeno</p> ... Show More
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Publication Date
Wed Oct 25 2023
Journal Name
Journal Of Optics
Integrated gallium phosphide-waveguide polarization rotator based on rotating a horizontal slot by 45 degree for 700 nm wavelength
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Polarization manipulation elements operating at visible wavelengths represent a critical component of quantum communication sub-systems, equivalent to their telecom wavelength counterparts. The method proposed involves rotating the optic axis of the polarized input light by an angle of 45 degree, thereby converting the fundamental transverse electric (TE0) mode to the fundamental transverse magnetic (TM0) mode. This paper outlines an integrated gallium phosphide-waveguide polarization rotator, which relies on the rotation of a horizontal slot by 45 degree at a wavelength of 700 nm. This will ultimately lead to the conception of a mode hybridization phenomenon in the waveguide. The simulation results demonstrate a polarization co

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Publication Date
Tue Dec 11 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Suggested Index for studying violent by Environment and Psychology components among Collegian students at a sample in Baghdad City
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Objective: To identification environmental and psychological violence's components among collegians’ students of different stages, and gender throughout creating specific questionnaire, and estimating regression of environmental domain effect on psychological domain, as well as measuring powerful of the association contingency between violence's domains in admixed form with respondent characteristics, such that (Demographics, Economics, and Behaviors), and extracting model of estimates impact of studied domains in studying risks, and protective factors among collegians’ students in Baghdad city. Methodolog

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Study of charge density distributions, elastic charge form factors and root-mean square radii for 4He, 12C and 16O nuclei using Woods- Saxon and harmonic-oscillator potentials
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The nuclear charge density distributions, form factors and
corresponding proton, charge, neutron, and matter root mean square
radii for stable 4He, 12C, and 16O nuclei have been calculated using
single-particle radial wave functions of Woods-Saxon potential and
harmonic-oscillator potential for comparison. The calculations for the
ground charge density distributions using the Woods-Saxon potential
show good agreement with experimental data for 4He nucleus while
the results for 12C and 16O nuclei are better in harmonic-oscillator
potential. The calculated elastic charge form factors in Woods-Saxon
potential are better than the results of harmonic-oscillator potential.
Finally, the calculated root mean square

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Study of charge density distributions, elastic charge form factors and root-mean square radii for 4He, 12C and 16O nuclei using Woods- Saxon and harmonic-oscillator potentials
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The nuclear charge density distributions, form factors andcorresponding proton, charge, neutron, and matter root mean squareradii for stable 4He, 12C, and 16O nuclei have been calculated usingsingle-particle radial wave functions of Woods-Saxon potential andharmonic-oscillator potential for comparison. The calculations for theground charge density distributions using the Woods-Saxon potentialshow good agreement with experimental data for 4He nucleus whilethe results for 12C and 16O nuclei are better in harmonic-oscillatorpotential. The calculated elastic charge form factors in Woods-Saxonpotential are better than the results of harmonic-oscillator potential.Finally, the calculated root mean square radii usingWoods-Saxonpotentials ho

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Publication Date
Fri Mar 31 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Effect of some Variables on the Formulation of Captopril as Tablets Shaymaa Nazar Al – Sammarrai
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Captopril is an angiotensin converting enzyme inhibitor (ACEI) used to treat hypertension,
congestive heart failure, and myocardial infraction.
The only dosage form available for captopril is the plain tablet in strength of 12.5,25,50 and 100mg
tablet.
This investigation is concerned with factors affecting the formulation of captopril as a plain
tablet dosage form of 50mg. Many trials were made to prepare satisfactory tablets for the drug by
using wet – granulation methods with various additives. It was found that poly vinyl pyrrolidone
(P.V.P.) as binder gave the most satisfactory tablets. At the same time a shorter disintegrantion time
and slower dissolution rate were obtained with the addition of starch

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