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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
Wed Feb 05 2003
Journal Name
. Sc. Conf. Of The College 5th Of Eng. Univ. Of Baghdad 2003
COMPUTATIONAL AND EXPERIMENTAL INVESTIGATION OF THE AERODYNAMIC CHARACTERISTICS FOR A FORWARD SWEPT WING AIRCRAFT
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The aerodynamic characteristics of the forward swept wing aircraft have been studied theoretically and experimentally. Low order panel method with the Dirichlet boundary condition have been used to solve the case of the steady, inviscid and compressible flow. Experimentally, a model was manufactured from wood to carry out the tests. The primary objective of the experimental work was the measurements of the wake dimensions and orientation, velocity defect along the wake and the wake thickness. A blower type low speed (open jet) wind tunnel was used in the experimental work. The mean velocity at the test section was (9.3 m/s) and the Reynolds number based on the mean aerodynamic chord and the mean velocity was (0.46x105). The measurements sho

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Publication Date
Tue Feb 21 2017
Journal Name
Biomechanics And Modeling In Mechanobiology
A novel method for non-invasively detecting the severity and location of aortic aneurysms
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The influence of an aortic aneurysm on blood flow waveforms is well established, but how to exploit this link for diagnostic purposes still remains challenging. This work uses a combination of experimental and computational modelling to study how aneurysms of various size affect the waveforms. Experimental studies are carried out on fusiform-type aneurysm models, and a comparison of results with those from a one-dimensional fluid–structure interaction model shows close agreement. Further mathematical analysis of these results allows the definition of several indicators that characterize the impact of an aneurysm on waveforms. These indicators are then further studied in a computational model of a systemic blood flow network. This demonstr

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Publication Date
Thu Feb 01 2024
Journal Name
American Journal Of Pharmaceutical Education
Academic Entitlement Among Pharmacy Students in the Arab World: A Multi-National Exploratory Study
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Publication Date
Sun Apr 28 2024
Journal Name
Bmc Medical Education
Pharmacy faculty experiences with student academic entitlement: a multinational study from the Arab world
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Abstract<p>Academic Entitlement (AE) is the expectation by students to receive high grades or preferential treatment without significant effort. Exploring AE from faculty perspective has not been investigated in Arab colleges of pharmacy. The aim of this study was to explore experiences and perceptions towards student AE among pharmacy faculty in the Arab World. A cross-sectional, self-administered, anonymous, electronic survey was sent to pharmacy faculty across pharmacy colleges in Arab countries. The survey collected demographic data, an AE measure including 17 items reflecting seven AE components, and faculty perceptions and perceived reasons for AE. A total of 345 responses were collected. The AE level wa</p> ... Show More
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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Aljdhiran incision and rip and derivatives in the Qur'an: A statistical study morphological tag
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It is more beneficial science and created and the highest honor is the Koran Sciences, God has honored research in this fun science, came this research that shed the light on the radical incision, and Naughty derivatives as contained in the Koran, and illustrate the diversity of Saghma morphological, and fork them from derivatives what it entailed connotations, as well as the evacuation of cryptic in some of these verses from the biological secrets take minds newly exposed Anitrjt science under the name of scientific miracles.
The research methodology is revenue verse which included the word, and revenue lexical meaning and its meaning in the context of the Qur'an, and reflect the views of the commentators of the verse, and then the r

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Publication Date
Fri Apr 01 2022
Journal Name
International Journal Of Pharmacy Practice
Exploring job satisfaction among pharmacy professionals in the Arab world: a multi-country study
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Abstract<sec> <title>Objectives

The study objectives were to (1) describe the characteristics of the pharmacy professionals and (2) explore the association between job satisfaction and factors, such as work control, work stress, workload and organization and professional commitments.

Methods

This study was a cross-sectional design. The survey items were mainly adapted from the US National Pharmacist Workforce Survey. An electronic (Qualtrics) questionnaire was posted on pharmacist social media in several A

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Publication Date
Tue Jan 01 2013
Journal Name
International Journal Of Contemporary Mathematical Sciences
Equivalent between the Criterion and the Three Open Set's Conditions in Disk-Cyclicity
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A vector in a separable infinite dimensional Hilbert space is called disk-cyclic for bounded operator if the orbit α : 0, α∈;|∝| 1is dense in. The useful tool used to discover codisk-cyclic operation is called the disk-cyclic Criterion. In this paper we will show that some equivalent conditions of the

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Publication Date
Thu Aug 29 2024
Journal Name
European Journal Of Orthodontics
Poly-ether-ether-ketone (PEEK) versus dead-soft coaxial bonded retainers: a randomized clinical trial. Part 1. Stability, retainer failure, and participant satisfaction
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Abstract<sec> <title>Background

Poly-ether-ether-ketone (PEEK) was introduced in dentistry as an alternative to metal alloys.

Objective

To assess the effectiveness of PEEK-fixed retainers in preserving the stability of mandibular anterior and participant satisfaction as compared to the Dead-soft coaxial fixed retainer (DSC).

Trial design

A single-centre, two-arm parallel groups

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Publication Date
Tue Aug 30 2022
Journal Name
Iraqi Journal Of Agricultural Sciences
ESTIMATING FACTORS AFFECTING WHEAT MARKETING EFFICIENCY USING TOBIT MODEL
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This study was aimed to measure marketing efficiency and study important factors affecting , using TOBIT qualitative response model for wheat crop in Salahalddin province. Results revealed that independent factors such as (marketing type, crops duration in the field, average marketing cost, distance between farm and marketing center, and average productivity) had an impact on wheat marketing efficiency. This impact varied in size and direction due to value of parameters. Values of marketing efficiency fluctuated within cities and towns in the province. The average value on the province level was 76.75%. This study was recommended developing marketing infrastructures which is essential to efficiency increases. In addition, it is impo

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Secure communications by chaotic carrier signal using Lorenz model
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In this paper, the generation of a chaotic carrier by Lorenz model
is theoretically studied. The encoding techniques has been used is
chaos masking of sinusoidal signal (massage), an optical chaotic
communications system for different receiver configurations is
evaluated. It is proved that chaotic carriers allow the successful
encoding and decoding of messages. Focusing on the effect of
changing the initial conditions of the states of our dynamical system
e.i changing the values (x, y, z, x1, y1, and z1).

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