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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 Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
Triumph in the Glorious Qur’an: A Semiotic study
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Triump is a happy end and a positive outcome of any good deed on the part of a human
being, or of any competition or contest in any field. A human being’s life abounds with gain
and loss. If one succeeds one will be happy psychologieally, physieally, etc. if one the other
hard one loses, one wil be in a state. Between loss and gain there are many a step.
However humans work hard to be a great success and a read winner.The life of the world constitutes a huge race-track where people try hard to head towards
the hereafter. Therefore, we find people who succed and gain the Garden, and people whose
habitation is the fire, The Glorious Qur’an has shown us in many a surah the way to success
when Allah mentions ‘great

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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The role of investment climate indicators in stimulating economic growth: a standard study For Malaysia 1990-2016
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In globalization, the world became open area to competition for the attractive of investment, and the abilities of each country to win the confidence of investors depend upon the preparation to optimize circumstances.   The competitiveness is an essential means of expanding the capacity of developed to coexist in an international environment characterized by globalization. While competition describes the market structure, the behavior of investors and business, competitiveness is interested in the evaluation of business performance or countries and compare them in the conditions of competition available in these markets. Regarding Malaysia, which is depend on FDI-Export- Led Growth strategy,  it has taking on diffe

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Publication Date
Sun Jan 01 2017
Journal Name
Engineering And Technology Journal
Study of the Diffusion Coefficient and Hardness for a Composite Material when Immersed in Different Solutions Polymer
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Publication Date
Tue Jul 22 2025
Journal Name
Journal Of Physical Education
A study of some variables biomechanics in clean and jerk for the world champions men and women
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Publication Date
Tue Jan 02 2018
Journal Name
Journal Of Educational And Psychological Researches
The Role of Social service in Addressing Social Problems Aversion for Teenagers (A field Study in Baghdad)
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Adolescence important and sensitive stage in social terms, being a stage where learns teenager bear social responsibilities and composition of their ideas about family life, as well as it is the stage where the teenager looking to himself for an important place in the community to become independent socially people, so it highlights the role of Social Work to do better effort and I believe him in order to prepare for the adolescent stage of adolescence and help him overcome the problems so that makes it adapts to the society in which he lives

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Publication Date
Thu Jan 02 2020
Journal Name
Indian Journal Of Forensic Medicine & Toxicology
A Comparative Evaluation of Gutta-Percha and Sealer Removal of Rotary Niti File Retreatment Systems
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Publication Date
Sat Jan 25 2020
Journal Name
Indian Journal Of Forensic Medicine & Toxicology
A Comparative Evaluation of Gutta-Percha and Sealer Removal of Rotary Niti File Retreatment Systems
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Forty lower premolars with single root canals prepared with ProtaperNext files to size 25, and obturated with GP/sealer using lateral compaction. Teeth divided randomly into four groups (group n=10). Protaper universal retreatment kit (PUR), D-Race desobturation files (DRD), R-Endo retreatment kit (RE) and Hedstrom (H) files (control) were used to remove GP/sealer in each group. Removal effectiveness assessed by measuring the GP /sealer remnants in the roots after sectioning them into two halves. Stereomicroscope with a digital camera used to capture digital images. Images processed by ImageJ software to measure the percentage of GP/sealer remnants surface area in total, coronal, middle and apical areas of the canal. In the coronal area,

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Role Of Smart Leadership Dimensions In Crisis Management- A study For Opinions Of Sample Of Administrative Leaderships In A number Of Humanities Colleges At The University Of Mosul
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This research aims at answering many questions raised by the research problem concerning the view of the organizations under consideration for the concept of smart leadership and its most important dimensions, as well as the view of crisis management and its concept and most important methods through research objectives that define and clarify the smart leadership with its dimensions and methods of crisis management.

For the purpose of reaching the results of the research and testing the assumptions about the relationship between smart leadership and methods of crisis management, the researcher adopted a questionnaire, designed especially to be a criterion for the research, as the main tool for data coll

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Publication Date
Wed Dec 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Correlation between Periodontal Health Status and Salivary Matrix Metalloproteinase-9 Levels in Smoker and Non-Smoker Chronic Periodontitis Patients (A Comparative Study)
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Background: Periodontal diseases are inflammatory diseases affecting the supporting tissues of the teeth. One of the leading environmental factors that are closely related not only to the risk but also to the prognosis of periodontitis is smoking. This study aimed to evaluate the influence of smoking on periodontal health status and to measure the levels of matrix metalloproteinase-9 in smokers and nonsmokers chronic periodontitis patients, also it aimed to test the correlation between the levels of matrix metalloproteinase-9 and the clinical periodontal parameters. Materials and Methods: Five milliliters samples of un-stimulated whole saliva and full-mouth clinical periodontal recordings (plaque index, gingival index, bleeding on probing,

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Publication Date
Sat Jan 01 2022
Journal Name
Education For Health
Determinants of social accountability for medical schools in Iraq: A qualitative case study
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