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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 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
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
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
Thu Jun 01 2017
Journal Name
American Journal Of Pharmaceutical Education
Exploring Electronic Communication Modes Between Iraqi Faculty and Students of Pharmacy Schools Using the Technology Acceptance Model
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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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Publication Date
Sun Sep 03 2017
Journal Name
Baghdad Science Journal
Kinetic and Mechanistic Studies for the Gas-phase Reaction of Ozone with 2, 3-Dimethyl-2-Butene and 1, 3-Butadiene
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The reactions of ozone with 2,3-Dimethyl-2-Butene (CH3)2C=C(CH3)2 and 1,3-Butadiene CH2=CHCH=CH2 have been investigated under atmospheric conditions at 298±3K in air using both relative and absolute rate techniques, and the measured rate coefficients are found to be in good agreement in both techniques used. The obtained results show the addition of ozone to the double bond in these compounds and how it acts as function of the methyl group substituent situated on the double bond. The yields of all the main products have been determined using FTIR and GC-FID and the product studies of these reactions establish a very good idea for the decomposition pathways for the primary formed compounds (ozonides) and give a good information for the effe

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Publication Date
Mon Apr 04 2011
Journal Name
Ibn Al-haitham J.for Pure &appl.sci
Anew Spectrophotometric Method For The Determination of La (III) With 3-Hydroxy -4-(2-hydroxy –Phenyl azo)Naphthalene -1-Sulfonic Acid
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A simple, rapid and sensitive spectrophotometric method has been proposed for the determination of La (III) using 3-hydroxy -4-(2-hydroxy-phenyl azo) naphthalene -1- sulfonic acid as a chromogenic reagent. This method is based on the formation of a red-pink colored complex, upon the reaction of La(III) with the reagent in an alkaline medium (pH= 9.50), having a maximum absorbance at 459 nm. Beer's law is valid in the concentration range 0.512 µg.ml-1 with a Sandell's sensitivity value of 0.0188 µg.cm-2 and molar absorptivity of 7376.12 L.mol-1.cm-1. The stoichiometric composition of the chelate is 1:3. The effect of the presence of different cations as interferants in the determination of La(III) under the given optimum conditions wer

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Publication Date
Sun Dec 02 2018
Journal Name
Journal Of The College Of Education For Women
The Role of Local Satellite Channels in the formation of knowledge and trends of the Iraqi Public Towards Terrorism: A Field Study
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Terrorism is a global phenomenon that engulfs most regions of the world to varying degrees. Media outlets are aware of the many incidents of violence and terrorism that have increased in recent times. The differences between the size of the phenomenon in different societies are the causes and severity of the phenomenon. On the role of local satellite channels in shaping the knowledge and trends of the Iraqi public towards the events of terrorism, in light of the assumptions of reliance on the media. The importance of this study is that it assesses the role of local satellite channels in the formation of knowledge and trends The study seeks to know the extent of exposure of the Iraqi public to local satellite channels, and to reveal the e

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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A proposed audit program for a comprehensive electronic banking system based on business risks : applied research
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The research seeks to identify the comprehensive electronic banking system and the role of the auditor in light of the customer's application of electronic systems that depend on the Internet in providing its services, as a proposed audit program has been prepared in accordance with international auditing controls and standards based on the study of the customer's environment and the analysis of external and internal risks in the light of financial and non-financial indicators, the research reached a set of conclusions, most notably, increasing the dependence of banks on the comprehensive banking system for its ability to provide new and diverse banking services, The researcher suggested several recommendations, the most important of whi

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