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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
Wed Dec 01 2010
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Technical methodology balanced performance as a strategic framework for the economic units operating in the Iraqi industrial sector environment
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facing economic units operating in the environment sector of the Iraqi

industrial many pressures in its seeking to measure and evaluate its performance because of variables, today's corporate environment, as the case which makes looking for a methodology can be adopted to evaluate its performance with a more holistic, rather than being limited to traditional measures that are no longer enough to keep pace with rapid changes in today's corporate environment, which requires that measures of performance are derived from the strategy of unity and commensurate with the specificity of the environment in Iraq. Try searching discussion Ttormwhrat and performance measurement systems to suit the business strategies and directions of change

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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
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
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
Fri Dec 31 2021
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
GEOMETRY OPTIMIZATION OF COUPLING ALLIN -METFORMIN USING DFT/B3LYP MOLECULAR MODELLING TECHNIQUE: GEOMETRY OPTIMIZATION OF COUPLING ALLIN -METFORMIN USING DFT/B3LYP MOLECULAR MODELLING TECHNIQUE
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This researchpaper includes the incorporation of Alliin at various energy levels and angles 

With Metformin using Gaussian 09 and Gaussian view 06. Two computers were used in this work. Samples were generated to draw, integrate, simulate and measure the value of the potential energy surface by means of which the lowest energy value was (-1227.408au). The best correlation compound was achieved between Alliin and Metformin through the low energy values where the best place for metformin to b

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Publication Date
Wed Jan 01 2020
Journal Name
Annals Of Tropical Medicine And Public Health
EFFECT OF EUCALYPTUS AND MYRTUS EXTRACTS IDENTIFICATION BY GAS CHROMATOGRAPHY-MASS SPECTROMETRY ON SOME SPECIES OF CANDIDA AS A MODEL OF MEDICAL PLANTS
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Publication Date
Wed Jun 10 2020
Journal Name
Annals Of Tropical Medicine & Public Health
EFFECT OF EUCALYPTUS AND MYRTUS EXTRACTS IDENTIFICATION BY GAS CHROMATOGRAPHY-MASS SPECTROMETRY ON SOME SPECIES OF CANDIDA AS A MODEL OF MEDICAL PLANTS
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The study showed that all extracts (aqueous, ethanolic and acetonic) of the leaves of Eucalyptus and Myrtus plants had a inhibitory effect on the growth of all types of yeasts studied, acetone extract recorded the highest inhibition of yeastat 100ppm concentration,The inhibition was 35mm, 34mm, 24mm and 20mm for Candida parapsilosis, Candida glabrata, Candida tropicalis and Candida albicans respectively, The experiments above showed the least significant differences at 0.05 level.The results ofE. Cammldulensis ethanolic tincture analysis has shown the presence of 44 biologically active substances. The main Eucalyptus leaves component was: 2-Bicyclo (2-2.1) heptanol (12.37%), Ledol (8.23%),1,2,4- Benzenetriol (8.45%) and that contain spathul

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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
Mon Oct 01 2018
Journal Name
International Journal Of Research In Social Sciences And Humanities
THE SOCIAL INTERACTION OF LANGUAGE IN A COMIC SERIES: A SOCIOLINGUISTIC STUDY
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Dell Hymesin 1964coined The Ethnography of Communication in an attempt to explain the ways in which people use the language to interact. It hypothesizes that ethnography is less applicable among participants who have the same sociocultural background. It was proven that all the basic speech components occur whenever there is an interactional situation. The elements of (SPEAKING) schema are closely connected. However, the findings establish the fact that these elements take place effectively among participants who have the same sociocultural background.One of the most outstanding conclusions is the capability of the (SPEAKING) model to analyze not only an interaction between two or more participants, but also any event which consists of a mo

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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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