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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 01 2023
Journal Name
International Journal Of Rheumatic Diseases
A 5 item version of the Workplace Activity Limitation Scale successfully identifies impaired work productivity in rheumatoid arthritis patients: A split‐sample factor analysis approach
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Abstract<sec><title>Background

There is a growing interest in studying the effects of arthritis on a person's work productivity using a growing variety of outcome indicators.

Objectives

To develop a valid and reliable shortened version of the Workplace Activity Limitation Scale 12 (WALS‐12) for assessing work productivity limitations in rheumatoid arthritis (RA) patients.

Methods

A cross‐sectional study involving 277 RA patients was conducted. An exploratory factor analysis on WALS‐12 was used for item reduction on the first sample. Then confirmatory factor ana

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Publication Date
Wed Aug 17 2022
Journal Name
Applied Sciences
Predicting Fruit’s Sweetness Using Artificial Intelligence—Case Study: Orange
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The manual classification of oranges according to their ripeness or flavor takes a long time; furthermore, the classification of ripeness or sweetness by the intensity of the fruit’s color is not uniform between fruit varieties. Sweetness and color are important factors in evaluating the fruits, the fruit’s color may affect the perception of its sweetness. This article aims to study the possibility of predicting the sweetness of orange fruits based on artificial intelligence technology by studying the relationship between the RGB values of orange fruits and the sweetness of those fruits by using the Orange data mining tool. The experiment has applied machine learning algorithms to an orange fruit image dataset and performed a co

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of Educational And Psychological Researches
The Effect of Using Waks Strategy Upon Acquisition The Psychological Concepts And Mind Habits for Students of College of Education
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  The aim of research is to identify the effect of using Waks strategy upon acquiring the psychological concepts and mind habits for students in the college of education. An experimental design with a partial adjustment of two experimental and control groups as well as a posttest were employed. The researcher divided the study sample into two groups: group one consisted of (38) students to represent the experimental group that was taught according to the waks strategy, and group two consisted of (35) students to represent the control group that was taught according to the traditional method. The sample was chosen based on some variables namely (Intelligence, Prior knowledge). The researcher has designed the research tools as th

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Publication Date
Tue Sep 11 2018
Journal Name
Iraqi Journal Of Physics
Estimation the annual dose for residents in the area around the berms of Al-Tuwaitha nuclear site using RESRAD software
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RESRAD is a computer model designed to estimate risks and radiation doses from residual radioactive materials in soil. Thirty seven soil samples were collected from the area around the berms of Al-Tuwaitha site and two samples as background taken from an area about 3 km north of the site. The samples were measured by gamma-ray spectrometry system using high purity germanium (HPGe) detector. The results of samples measurements showed that three contaminated area with 238U and 235U found in the study area. Two scenarios were applied for each contaminated area to estimate the dose using RESRAD (onsite) version 7.0 code. The total dose of resident farmer scenario for area A, B and C are 0.854, 0.033 and 2.15×10-3 mSv.yr-1, respectively. Whi

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Publication Date
Sat Feb 03 2018
Journal Name
Chinese Journal Of Physics
A true random number generator based on the photon arrival time registered in a coincidence window between two single-photon counting modules
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True random number generators are essential components for communications to be conconfidentially secured. In this paper a new method is proposed to generate random sequences of numbers based on the difference of the arrival times of photons detected in a coincidence window between two single-photon counting modules

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Publication Date
Fri Jan 01 2021
Journal Name
Chemical Industry And Chemical Engineering Quarterly
Electrochemical harvesting of microalgae꞉ Parametric and cost-effectivity comparative investigation
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The cost of microalgae harvesting constitutes a heavy burden on the commercialization of biofuel production. The present study addressed this problem through economic and parametric comparison of electrochemical harvesting using a sacrificial electrode (aluminum) and a nonsacrificial electrode (graphite). The harvesting efficiency, power consumption, and operation cost were collected as objective variables as a function of applied current and initial pH of the solution. The results indicated that high harvesting efficiency obtained by using aluminum anode is achieved in short electrolysis time. That harvesting efficiency can be enhanced by increasing the applied current or the electrolysis time for both electrode materials, where 98

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Publication Date
Thu Aug 29 2024
Journal Name
Materials
Experimental Study to Investigate the Performance-Related Properties of Modified Asphalt Concrete Using Nanomaterials Al2O3, SiO2, and TiO2
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The dual nature of asphalt binder necessitates improvements to mitigate rutting and fatigue since it performs as an elastic material under the regime of rapid loading or cold temperatures and as a viscous fluid at elevated temperatures. The present investigation assesses the effectiveness of Nano Alumina (NA), Nano Silica (NS), and Nano Titanium Dioxide (NT) at weight percentages of 0, 2, 4, 6, and 8% in asphalt cement to enhance both asphalt binder and mixture performance. Binder evaluations include tests for consistency, thermal susceptibility, aging, and workability, while mixture assessments focus on Marshall properties, moisture susceptibility, resilient modulus, permanent deformation, and fatigue characteristics. NS notably im

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Publication Date
Thu Aug 29 2024
Journal Name
Materials
Experimental Study to Investigate the Performance-Related Properties of Modified Asphalt Concrete Using Nanomaterials Al2O3, SiO2, and TiO2
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The dual nature of asphalt binder necessitates improvements to mitigate rutting and fatigue since it performs as an elastic material under the regime of rapid loading or cold temperatures and as a viscous fluid at elevated temperatures. The present investigation assesses the effectiveness of Nano Alumina (NA), Nano Silica (NS), and Nano Titanium Dioxide (NT) at weight percentages of 0, 2, 4, 6, and 8% in asphalt cement to enhance both asphalt binder and mixture performance. Binder evaluations include tests for consistency, thermal susceptibility, aging, and workability, while mixture assessments focus on Marshall properties, moisture susceptibility, resilient modulus, permanent deformation, and fatigue characteristics. NS notably im

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Publication Date
Thu Dec 01 2022
Journal Name
Scientific Research Journal Of Engineering And Computer Science
Cryptography Techniques - A Review
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Publication Date
Thu Sep 15 2022
Journal Name
Al-adab Journal
Towards a Humanitarian Race
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