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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
Thu Aug 16 2018
Journal Name
International Journal Of Research In Social Sciences And Humanities
The Social Interaction of Langauge in a Comic Series: A Sociolinguistic Study
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DBNRAHA Hameed, IJRSSH PUBLICATION, 2018

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Publication Date
Tue Feb 18 2025
Journal Name
International Journal Of Scientific Research In Science, Engineering And Technology
A Comprehensive Review on Cryptography Algorithms: Methods and Comparative Analysis
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The evolution of cryptography has been crucial to preservation subtle information in the digital age. From early cipher algorithms implemented in earliest societies to recent cryptography methods, cryptography has developed alongside developments in computing field. The growing in cyber threats and the increase of comprehensive digital communications have highlighted the significance of selecting effective and robust cryptographic techniques. This article reviews various cryptography algorithms, containing symmetric key and asymmetric key cryptography, via evaluating them according to security asset, complexity, and execution speed. The main outcomes demonstrate the growing trust on elliptic curve cryptography outstanding its capabi

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Advanced Pharmacy Education And Research
Comparative biosimilar quality studies between a rituximab product and MabThera
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Publication Date
Sun Jan 24 2016
Journal Name
Al-academy
Experimentation in caves painting (A comparative analysis): فريد خالد علوان
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Addressed the problem of the research is marked (experimentation in caves fee) concept and its role in experimentation deviate Display Num formal charges caves. The search came in four sections: general framework for research and identified the research problem and the need for him. With an indication of the importance of his presence. Then specify the search for the goals of (revealed the nature and role of experimentation in determining the nature of Manifesting fee documented on the walls of caves), followed by the establishment of the three search limits (objectivity, the temporal and spatial) were then determine the terms related to the title. Then provide the theoretical framework and indicators that resulted from academic theorizi

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Role of External Audit in Limiting Creative Accounting Practices in Light of International Standards from The Point of View of Certified Accountancy Experts in Iraq as a Model
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This research aims to solve a problem in the field of accounting and financial knowledge in the world today, that is, the problem of creative accounting. Especially after the global financial crisis and the collapse of many large companies in the world, people find that they use creative accounting methods to distinguish them from reality, showing the results of their activities and their financial status. This research discusses the concept of creative accounting, the most important methods used in financial statements and its relationship with external auditing, and procedures to limit accounting creativity. This study uses descriptive analysis methods after confirming its theoretical aspects in practice. Using the statistical

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Publication Date
Tue May 16 2023
Journal Name
International Journal Of Online And Biomedical Engineering (ijoe)
Comparative Study of Anemia Classification Algorithms for International and Newly CBC Datasets
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Data generated from modern applications and the internet in healthcare is extensive and rapidly expanding. Therefore, one of the significant success factors for any application is understanding and extracting meaningful information using digital analytics tools. These tools will positively impact the application's performance and handle the challenges that can be faced to create highly consistent, logical, and information-rich summaries. This paper contains three main objectives: First, it provides several analytics methodologies that help to analyze datasets and extract useful information from them as preprocessing steps in any classification model to determine the dataset characteristics. Also, this paper provides a comparative st

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Publication Date
Sun May 15 2022
Journal Name
Bionatura
Comparative anatomical study to skeleton for same species of Turtles in Iraq
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Bones were recorded in the skeleton of some species of Iraqi turtle Mauremys rivulata; the objectives of this study came in light of current conditions, environmental developments, talents and techniques of biological studies taking place in the country, need for an anatomy guide in river turtles of Iraqi species, to identify all kinds of similarities and differences with their preaching, this work or study has become written in response to those modern needs. It is designed to be one of the resources for those interested in biological studies, beginners or professionals, and veterinarians, distinguishing them from marine and global species. Turtles were dissected in the laboratories of the Research Center and Museum of Natural Hist

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Publication Date
Fri Mar 31 2017
Journal Name
Journal Of Engineering
Cultivation of Chlorella Vulgaris Using Airlift Photobioreactor Sparged with 5%CO 2 -Air as a Biofixing Process
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The present paper addresses cultivation of Chlorella vulgaris microalgae using airlift photobioreactor that sparged with 5% CO 2 /air. The experimental data were compared with that obtained from bioreactor aerated with air and unsparged bioreactor. The results showed that the concentration of biomass is 0.36 g l -1  in sparged bioreactor with CO2/air, while, the concentration of biomass reached to 0.069 g l -1  in the unsparged bioreactor. They showed also that aerated  ioreactor.with CO2/air gives more biomass production even the bioreactor was aerated with air. This study proved that application of sparging system for  ultivation of Chlorella vulgaris microalgae using either CO2/air mixture or air has a significant

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Publication Date
Sat Dec 31 2022
Journal Name
Al-kindy College Medical Journal
The Efficiency of Corn Solution as a Cytological Fixative in Buccal Smear : Corn Solution as Cytological Fixative
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Background: Corn Syrup is food syrup higher of carbohydrate, depending on grade. The study aimed to assess efficiency of Corn syrup as cytological fixative.

Subjects and methods: This was laboratory based study, it has been conducted at Elrazi University included   apparently 30 healthy students have been involved in this study.

Results: Out of 30 smears fixed with 95% alcohol, 76.7% (n=23) shows excellent nuclear stain, 23.3% (n= 7)   shows good nuclear stain. 70% (n=21) show excellent cytoplasmic stain, 26.7% (n=8) shows good cytoplasmic stain, 3.3% (n=1) shows poor cytoplasmuc stain.

   Out of 30 smears fixed with corn solution, 60

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Publication Date
Sun Jul 01 2012
Journal Name
Journal Of Techniques مجلة التقني
A STUDY OF SOME TECHNICAL AND ECONOMICAL PARAMETERS FOR MACHINERY UNIT (NEW HOLLAND &DISC PLOW) BY USING THREE DIFFERENT TILT ANGLES دراسة بعض المؤشرات الفنية والأقتصادية للوحدة الميكنية (الجرار نيوهولاند مع المحراث القرصي الثلاثي القلاب) بأستخدام زوايا ميل مختلفة للأقراص
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