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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
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Working Memory Classification Enhancement of EEG Activity in Dementia: A Comparative Study
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The purpose of the current investigation is to distinguish between working memory ( ) in five patients with vascular dementia ( ), fifteen post-stroke patients with mild cognitive impairment ( ), and fifteen healthy control individuals ( ) based on background electroencephalography (EEG) activity. The elimination of EEG artifacts using wavelet (WT) pre-processing denoising is demonstrated in this study. In the current study, spectral entropy ( ), permutation entropy ( ), and approximation entropy ( ) were all explored. To improve the  classification using the k-nearest neighbors ( NN) classifier scheme, a comparative study of using fuzzy neighbourhood preserving analysis with -decomposition ( ) as a dimensionality reduction technique an

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Publication Date
Wed Sep 22 2021
Journal Name
International Journal Of Corrosion And Scale Inhibition
Synthesis of a CoO–ZnO nanocomposite and its study as a corrosion protection coating for stainless steel in saline solution
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Reaxys Chemistry database information SciVal Topics Metrics Abstract A novel CoO–ZnO nanocomposite was synthesized by the photo irradiation method using a solution of cobalt and zinc complexes and used as a coating applied by electrophoretic deposition (EPD) for corrosion protection of stainless steel (SS) in saline solution. The samples were characterized using powder XRD, scanning electron microscopy (SEM) and electrochemical polarization. It was also found that the coating was still stable after conducting the corrosion test: it contained no cracks and CoO–ZnO nanocomposites clearly appeared on the surface. SEM showed that the significant surface cracking disappeared. XRD confirmed that CoO–ZnO nanocomposites comprised CoO and Zn

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Publication Date
Wed Nov 05 2014
Journal Name
International Journal Of Applied Mathematical Research
Approximate solution of a model describing biological species living together using a new iterative method
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Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
A Comparative Study on Association Rule Mining Algorithms on the Hospital Infection Control Dataset
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Administrative procedures in various organizations produce numerous crucial records and data. These
records and data are also used in other processes like customer relationship management and accounting
operations.It is incredibly challenging to use and extract valuable and meaningful information from these data
and records because they are frequently enormous and continuously growing in size and complexity.Data
mining is the act of sorting through large data sets to find patterns and relationships that might aid in the data
analysis process of resolving business issues. Using data mining techniques, enterprises can forecast future
trends and make better business decisions.The Apriori algorithm has bee

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Publication Date
Mon Dec 03 2018
Journal Name
Journal Of Engineering
Similarity and Difference between Sustainable and Green Architecture (a Comparative Study)
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The research is concerned with studying the characteristics of Sustainable Architecture and Green Architecture, as a general research methodology related to the specific field of architecture, based on the differentiation between two generic concepts, Sustainability and Greening, to form the framework of the research specific methodology, where both concepts seem to be extremely overlapping for research centers, individuals, and relevant organizations. In this regard, the research tend towards searching their characteristics and to clearly differentiates between the two terms, particularly in architecture, where the research seeks understanding sustainable and green architectures, how they are so close or so far, and the

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Publication Date
Thu Jun 30 2011
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A PARTICULAR SOLUTION OF THE TWO AND THREE DIMENSIONAL TRANSIENT DIFFUSION EQUATIONS
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A particular solution of the two and three dimensional unsteady state thermal or mass diffusion equation is obtained by introducing a combination of variables of the form,
η = (x+y) / √ct , and η = (x+y+z) / √ct, for two and three dimensional equations
respectively. And the corresponding solutions are,
θ (t,x,y) = θ0 erfc (x+y)/√8ct and θ( t,x,y,z) =θ0 erfc (x+y+z/√12ct)

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Publication Date
Wed Oct 11 2023
Journal Name
Journal Of Educational And Psychological Researches
Teaching Problems Faced by Female Teachers of Students with Intellectual Disability in Special Education Programs and the Proposed Solutions for that from their point of view - a qualitative study
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This study aims to identify the teaching problems that teachers of students with intellectual disabilities face, in addition to exploring the solutions suggested by them in order to overcome such problems or challenges. The researchers used a qualitative approach in order to understand the teachers' perceptions about these problems in a more in-depth way. The interview tools (in-depth and semi-structured interviews) were used to collect data from (3) female teachers from special education programs in the Asir region. The results revealed a number of themes including problems related to students, teachers and the teaching methods they use, curricula, school environment, and school administration. Moreover, the results indicated that famil

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
PHARAOH'S CHARACTER BETWEEN THE QUR'ANIC TEXT AND THE ARABIC NOVEL: (Naguib Mahfouz's Pharaonic Novels as a Model)
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The Character is one of the elements of Storytelling, as it is the center of the plot, making it the basis on which the talk is about. The talk is the portrayal of the character while they’re acting; the novelist presents the character by interacting with the events, and the extent of the negative and positive appearing impact on the character. It should be noted that everyone has two personalities or more, each one appearing in a different position or situation. For instance, a man can be a father, a lover, an employee, a son or anyone else .. in another position, he might be a master, and in another a looser begging for the mercy of his humiliator, and sometimes he can show weakness to the one he loves, or show strength to his enemie

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Publication Date
Tue Apr 02 2024
Journal Name
Journal Of Engineering
Revolutionizing Depth Sensing: A Review Study of Apple LiDAR Sensor for as-built Scanning Applications
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Incorporating the LiDAR sensor in the most recent Apple devices represents a substantial development in 3D mapping technology. Meanwhile, Apple's Lidar is still a new sensor. Therefore, this article reviews the potential uses of the Apple Lidar sensor in various fields, including engineering and construction, focusing on indoor and outdoor as-built 3D mapping and cultural heritage conservation. The affordable cost and shorter observation times compared to traditional surveying and other remote sensing techniques make the Apple Lidar an attractive choice among scholars and professionals. This article highlights the need for continued research on the Apple LiDAR sensor technology while discussing its specifications and limitations. A

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Publication Date
Fri Nov 01 2019
Journal Name
Recent Technologies In Sustainable Materials Engineering
A Comparative Study Between the Individual, Dual and Triple Addition of (S.F.), (T.G.P.) and (P.V.A.) for Improving Local Gypsum (Juss) Properties
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