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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
Sun Jul 01 1990
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
KEY TO THE SPECIES OF THE GENUS STACHYS L. (LABIATAE) IN IRAQ WITH THREE NEW RECORDS
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A simplified parallel key was presented in this work for the Taxa of Stackys L. wildly grown in Iraq. Three records within this genus were newly recorded to our country in the present work and they are S. kermanshahansis Rech S. setifera C.A. Mey. subsp setifera, S. setifera ssp iranica (Reck.) The characteristics of these new records were also given with some representative specimens.

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Publication Date
Mon Jun 01 2020
Journal Name
Journal Of The College Of Languages (jcl)
A study of some of the of the Verbs’ Arabic Roots in the stories of Osman Ceviksoy Like a Voice in The Dark.: Osman Çeviksoy'un "Karanlıkta Ses Gibi" Başlıklı Öykü Kitabında Arapça Kökenli Türkçe Fillerin İncelenmesi
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Due to the Geographical links, language is one of the multiple affects among Arabs and Turks. As the different studies demonstrate, Turkish contains many words derived from other languages, yet Arabic remains the language that has great affects on Turkish. Unlike Turkish language, Arabic is a derivative language that requires no suffixes. Thus, Arabic verbs are tuned into Turkish verbs by adding auxiliary verbs. The present study traces some of the Turkish compound words of Arabic roots with an explanation that shows the Auxiliary added to form the Turkish verb as found in the stories of Otman Chevek Sawy’s Like A voice in the Dark. The conclusion sums up the findings of the study illustrated by numbers.

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Publication Date
Fri Mar 12 2021
Journal Name
Sensors
A Robust Handwritten Numeral Recognition Using Hybrid Orthogonal Polynomials and Moments
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Numeral recognition is considered an essential preliminary step for optical character recognition, document understanding, and others. Although several handwritten numeral recognition algorithms have been proposed so far, achieving adequate recognition accuracy and execution time remain challenging to date. In particular, recognition accuracy depends on the features extraction mechanism. As such, a fast and robust numeral recognition method is essential, which meets the desired accuracy by extracting the features efficiently while maintaining fast implementation time. Furthermore, to date most of the existing studies are focused on evaluating their methods based on clean environments, thus limiting understanding of their potential a

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Publication Date
Mon Jun 26 2023
Journal Name
Asia-pacific Journal Of Chemical Engineering
Sustainable environment through using porous materials: A review on wastewater treatment
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Abstract<p>Porous materials play an important role in creating a sustainable environment by improving wastewater treatment's efficacy. Porous materials, including adsorbents or ion exchangers, catalysts, metal–organic frameworks, composites, carbon materials, and membranes, have widespread applications in treating wastewater and air pollution. This review examines recent developments in porous materials, focusing on their effectiveness for different wastewater pollutants. Specifically, they can treat a wide range of water contaminants, and many remove over 95% of targeted contaminants. Recent advancements include a wider range of adsorption options, heterogeneous catalysis, a new UV/H<sub>2</sub>O<j></j></p> ... Show More
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Publication Date
Wed Mar 16 2022
Journal Name
2022 Muthanna International Conference On Engineering Science And Technology (micest)
A hybrid feature selection technique using chi-square with genetic algorithm
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Publication Date
Fri Jul 12 2024
Journal Name
International Journal Of Advances In Scientific Research And Engineering (ijasre), Issn:2454-8006, Doi: 10.31695/ijasre
A Proposed Blockchain-Based Digital-Identity Management using ERC 725/735
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In modern technology, the ownership of electronic data is the key to securing their privacy and identity from any trace or interference. Therefore, a new identity management system called Digital Identity Management, implemented throughout recent years, acts as a holder of the identity data to maintain the holder’s privacy and prevent identity theft. Therefore, an overwhelming number of users have two major problems, users who own data and third-party applications will handle it, and users who have no ownership of their data. Maintaining these identities will be a challenge these days. This paper proposes a system that solves the problem using blockchain technology for Digital Identity Management systems. Blockchain is a powerful techniqu

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Computer And Communications
Pathfinding in Strategy Games and Maze Solving Using A* Search Algorithm
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Publication Date
Mon Jan 01 2024
Journal Name
Explainable Artificial Intelligence In The Digital Sustainability Administration
Artificial Intelligence and Trends Using in Sustainability Audit: A Bibliometric Analysis
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Publication Date
Fri Sep 16 2022
Journal Name
Sustainability
Intellectual Capital History and Trends: A Bibliometric Analysis Using Scopus Database
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This article aims to provide a bibliometric analysis of intellectual capital research published in the Scopus database from 1956 to 2020 to trace the development of scientific activities that can pave the way for future studies by shedding light on the gaps in the field. The analysis focuses on 638 intellectual capital-related papers published in the Scopus database over 60 years, drawing upon a bibliometric analysis using VOSviewer. This paper highlights the mainstream of the current research in the intellectual capital field, based on the Scopus database, by presenting a detailed bibliometric analysis of the trend and development of intellectual capital research in the past six decades, including journals, authors, countries, inst

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Publication Date
Sun Aug 31 2025
Journal Name
Journal Of Science In Medicine And Life
Serum Endothelial Specific Molecule 1(EMS 1) and Uric Acid Levels in Severe Preeclampsia
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