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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 Oct 02 2016
Journal Name
Journal Of Educational And Psychological Researches
Teaching Problems facing the first three class teachers in the city of Buraimi
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The present study aimed to identify teaching problems which facing the teachers for first three grades classes, and if these problems different according to some variables teacher qualification, experience period, class grade). The study sample consist of (137 )

 female teachers who teach the first three grades in Braimy city in Oman, teachers spread in five government schools. Both researchers developed questionnaire to measure problems faced by the mentioned teachers, consist of 50 questions distributed into 4 dimensions (teacher, students, the curriculum, the evaluations), Also researchers checked questionnaire validity and stability. The results indicate to: The most common probl

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Publication Date
Mon Jan 01 2024
Journal Name
Communications In Mathematical Biology And Neuroscience
The contribution of amensalism and parasitism in the three-species ecological system's dynamic
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Publication Date
Wed Mar 23 2022
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a Training Program for the Development of Moral Intelligence among Preparatory Students
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This current research aims to identify the effectiveness of a training program in developing moral intelligence and mutual social confidence among middle school students. The researcher made a number of hypotheses for this purpose to achieve the goal of the research.                             

The researcher relied on the (Al Zawaida 2011) scale prepared according to Coles (1997), including (60) items, and the mutual social trust scale for (Nazmi 2001) based on Roter's theory including (38) items.               &nbsp

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Publication Date
Wed Jun 30 2004
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
The Analysis of a Fixed Bed Absorber Used for the Removal of Pollutants from Water
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Publication Date
Fri Mar 01 2024
Journal Name
Annales Pharmaceutiques Françaises
Adopting video assignments as a tool to improve first-year pharmacy students class engagement
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Publication Date
Sun Oct 01 2023
Journal Name
Minerva Dental And Oral Science
Salivary interleukin-1β as a biomarker to differentiate between periodontal health, gingivitis, and periodontitis
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Publication Date
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Anti CD20 Monoclonal Antibody (Rituximab) as a Rescue Treatment in Severe and Refractory SLE
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Systemic lupus erythematosus (SLE) is an autoimmune disease with polymorphic expression. B cells have an essential contribution in immune system activation via the production of different cytokines and functioning as potent antigen-presenting cells. Therefore, a drug that particularly targets B cells may represent an ideal therapeutic approach for SLE. Rituximab (RTX), an anti-CD20 monoclonal antibody causing transient B-cell depletion, has been used to manage SLE. This study aims to assess Rituximab effects on lupus nephritis (LN) patients when added to conventional immunosuppressants. Twenty four patients, 15-32 years old, with class III/IV/V LN were involved in this study. All were on steroids before lupus nephritis occurrence. They were

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Publication Date
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Anti CD20 Monoclonal Antibody (Rituximab) as a Rescue Treatment in Severe and Refractory SLE
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Systemic lupus erythematosus (SLE) is an autoimmune disease with polymorphic expression. B cells have an essential contribution in immune system activation via the production of different cytokines and functioning as potent antigen-presenting cells. Therefore, a drug that particularly targets B cells may represent an ideal therapeutic approach for SLE. Rituximab (RTX), an anti-CD20 monoclonal antibody causing transient B-cell depletion, has been used to manage SLE. This study aims to assess Rituximab effects on lupus nephritis (LN) patients when added to conventional immunosuppressants. Twenty four patients, 15-32 years old, with class III/IV/V LN were involved in this study. All were on steroids before lupus nephritis occurrence. They were

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Publication Date
Wed May 10 2017
Journal Name
Journal Of The College Of Languages (jcl)
Technical methods in foreign language teaching as a new method in foreign language learning
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Unter dem Titel " Technische Methoden im Fremdsprachunterricht als eine neueste Methode im Fremdsprachlernen, die Spiele als Muster"

versteht man, dass die Forschung  sich mit einer neuen Methoden im Fremdsprachunterricht beschäftigt. Von den neuen Methoden im Unterricht sind die Spiele. So man sieht  in den letzten Jahren viele Artikel zum Thema Spiele im Fremdsprschunterricht. Davon gehen wir aus, dass die Spiele im Unterricht eine groβe Rolle spielt, denn diese Methode macht Lust, Spaβ im Lernenprozeβ. Die Spiele im Unterricht bezeichnen als ein Mittel, um Unterricht etwas Schönes , Nützliches und Lebendigs zu sein. Die Spiele sind vielfälltig und unterscheidet sich nach den Themen und Materialien. In dieser F

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Publication Date
Tue Jun 30 2020
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
RATIONALIZATION OF CONSUMPTION AND ITS IMPACT ON ECONOMIC DEVELOPMENT (A PRELIMINARY STUDY): RATIONALIZATION OF CONSUMPTION AND ITS IMPACT ON ECONOMIC DEVELOPMENT (A PRELIMINARY STUDY)
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The research deals with the concept of rationalization of consumption, which is legitimately legitimized, by indicating the permissibility of consumption and its limits in Islam, the legitimate aspects of spending and its controls, and the concept of development in the Islamic economy. The researcher followed the descriptive method by presenting the legal texts and jurisprudential opinions and linking them to contemporary economic problems.The research has reached several conclusions, the most important of which is that the goal of Islam in relation to consumption is to inform the Muslim of the amount of economic maturity, and the truth of alms is good in money and religion. It is necessary for achieving maturity that both means

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