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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 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
Wed May 01 2024
Journal Name
Journal Of Physics: Conference Series
A modified ARIMA model for forecasting chemical sales in the USA
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Abstract<p>model is derived, and the methodology is given in detail. The model is constructed depending on some measurement criteria, Akaike and Bayesian information criterion. For the new time series model, a new algorithm has been generated. The forecasting process, one and two steps ahead, is discussed in detail. Some exploratory data analysis is given in the beginning. The best model is selected based on some criteria; it is compared with some naïve models. The modified model is applied to a monthly chemical sales dataset (January 1992 to Dec 2019), where the dataset in this work has been downloaded from the United States of America census (www.census.gov). Ultimately, the forecasted sales </p> ... Show More
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Publication Date
Sun Dec 02 2018
Journal Name
Journal Of The College Of Education For Women
Poverty and its Relations to Some Social Variables (Children in the Primary Stage as a Model)
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The phenomenon of poverty is one of the most important phenomena facing the world at large. Despite the tremendous technological progress witnessed by mankind and despite the unprecedented high levels of world economic production, poverty remains the greatest challenge facing the world. Statistics and studies have shown that poverty is caused by several problems: (health, social, economic, educational, etc.) These problems are obstacles to the ability to obtain employment opportunities, which leads in the beginning to the growth phenomenon of unemployment, and ultimately to the growth of poverty.

The results of a range of research in the field of psychology have confirmed that children from poor homes suffer from a high level of

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Publication Date
Sat Dec 17 2022
Journal Name
Applied Sciences
A Hybrid Artificial Intelligence Model for Detecting Keratoconus
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Machine learning models have recently provided great promise in diagnosis of several ophthalmic disorders, including keratoconus (KCN). Keratoconus, a noninflammatory ectatic corneal disorder characterized by progressive cornea thinning, is challenging to detect as signs may be subtle. Several machine learning models have been proposed to detect KCN, however most of the models are supervised and thus require large well-annotated data. This paper proposes a new unsupervised model to detect KCN, based on adapted flower pollination algorithm (FPA) and the k-means algorithm. We will evaluate the proposed models using corneal data collected from 5430 eyes at different stages of KCN severity (1520 healthy, 331 KCN1, 1319 KCN2, 1699 KCN3 a

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Publication Date
Mon Oct 07 2019
Journal Name
Construction Innovation
A hybrid conceptual model for BIM in FM
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Purpose

The purpose of this paper is to develop a hybrid conceptual model for building information modelling (BIM) adoption in facilities management (FM) through the integration of the technology task fit (TTF) and the unified theory of acceptance and use of technology (UTAUT) theories. The study also aims to identify the influence factors of BIM adoption and usage in FM and identify gaps in the existing literature and to provide a holistic picture of recent research in technology acceptance and adoption in the construction industry and FM sector.

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Publication Date
Thu Sep 30 2010
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
USING ALUMINUM REFUSE AS A COAGULANT IN THE COAGULATION AND FLIOCCULATION PROCESSES
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The present work aims to study the efficiency of using aluminum refuse, which is available locally (after dissolving it in sodium hydroxide), with different coagulants like alum [Al2 (SO4)3.18H2O], Ferric chloride FeCl3 and polyaluminum chloride (PACl) to improve the quality of water. The results showed that using this coagulant in the flocculation process gave high results in the removal of turbidity as well as improving the quality of water by precipitating a great deal of ions causing hardness. From the experimental results of the Jar test, the optimum alum dosages are (25, 50 and 70 ppm), ferric chloride dosages are (15, 40 and 60 ppm) and polyaluminum chloride dosages were (10, 35 and 55 ppm) for initial water turbidity (100, 500 an

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Publication Date
Thu Dec 22 2022
Journal Name
Fine Art Journal
Spatial relationships and their impact on monumental sculptures (arab capitals as a model)
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The current research deals with spatial relations as a tool to link urban landmarks in a homogeneous composition with monumental sculptures, by identifying these landmarks and the extent of their impact on them, which constitutes an urgent need to evaluate the appropriate place and its effects on them, so that this analytical study is a critical approach adopted in artistic studies of monumental models in Arabcapitals .The current research came in four chapters, the first chapter of which dealt with the research problem, its importance and the need for it, then its objectives that were determined in revealing the spatial relations and their impact on

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Publication Date
Thu Dec 01 2022
Journal Name
Advances In Cancer Biology - Metastasis
CX3CL1 as potential immunotherapeutic tool for bone metastases in lung cancer: A preclinical study
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Publication Date
Sun Aug 03 2025
Journal Name
Journal Of Baghdad College Of Dentistry
The effect of curvature angle and rotational speed on the cyclic fatigue of three types of rotary instrument (In vitro): comparative study
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Background: The fracture of instruments within root canal during endodontic treatment is a common incidence, fracture because of fatigue through flexure occurs due to metal fatigue, this study aimed to assess the effect of curvature angle and rotational speed on the cyclic fatigue of different type of Endodontic NiTi Rotary Instruments and compare among them. Materials and method: Three types of rotary instruments with tip size 0.25: ProTaPer F2 (Densply, Malifier) Revo-S SU( 0.06 taper, MicroMega) and RaCe system (0.06 taper, FKG, Dentaire), Forty file of each instrument were used within two canals with angle of curvature (40 &60 )at two speed (250&400)RPM, twelve group were formed for all instruments(total number=120),ten file fo

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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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