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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
Tue Dec 01 2015
Journal Name
Journal Of Engineering
Experimental Evaluation Use of Semifluidized Bed Adsorber for the Treatment of P-chlorophenol and O-cresol in Wastewater using Activated Carbon as Adsorbent
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In the present work the performance of semifluidized bed adsorber was evaluated for removal of phenolic compound from wastewater using commercial activated carbon as adsorbent. P-chlorophenol (4-Chlorophenol) and o-cresol (2-methylphenol) was selected as a phenolic compound for that purpose. The phenols percent removal, in term of breakthrough curves were studied as affected by hydrodynamics limitations which include minimum and maximum semifluidization velocities and packed bed formation in the column by varying various parameters such as inlet liquid superficial velocity (from Uminsf to 8Uminsf m/s), and retaining grid (sometimes referred to as adsorbent loading) to initial static bed height ratio (from 3-4.5). In

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Publication Date
Fri Jul 21 2023
Journal Name
Journal Of Engineering
Development A Method For Production Of Carbon Nanotubes
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In this work chemical vapor deposition method (CVD) for the production of carbon nanotubes (CNTs) have been improved by the addition of S. Steel mesh container (SSMC) inside which the catalyst (Fe/Al2O3) was placed. Scanning electron microscopy (SEM) investigation method used to study nanotubes produced, showed that high yield of two types of (CNTs) obtained, single wall carbon nanotube (SWCNTs) with diameter and length of less than 50nm and several micrometers respectively and nanocoil tubes with a diameter and length of less than 100nm and several micrometers respectively. The chemical analysis of (CNTs) reveals that the main component is carbon (94%) and a little amount of Al (0.32%), Fe (2.22%) the reminder is oxygen. It was also fou

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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
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
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
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
Wed Feb 18 2026
Journal Name
Jornal Of Al-muthanna For Agricultural Sciences
A Proposed Approach to Agricultural Extension in Iraq for a Better Response to the Needs of farmer’s to Address Their Challenges
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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
A study copepoda invertebrates ecology in lower Zab
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The samples were collected monthly crustaceans Mjmafah foot of two stations in tributary Zab down and two others in the Tigris River for one year with effect from November 2001 until October 2002 recorded during the study period the current 41 units taxonomic and were higher density of Mjmafah foot Guy Tigris River before the mouth of the tributary

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Publication Date
Sun Dec 01 2024
Journal Name
كلية التربية للبنات
Strategic Maneuvering in Commercial Advertisement: A Pragmatic Study
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This study deals with strategic maneuvering in advertisement from a pragmatic point of view found in some commercial advertisements in order to investigate and analyze the pragmatic devices that are used in the strategic maneuvering and stages. The study attempts to shed light on the most fuzzy areas in advertisements that is probably how the language of advertisements employed by advertisers to affect consumers positively. The primary goal of strategic maneuvering is to discover how the pragmatic devices have persuasive techniques that are used to gain a competitive advantage and more sales. This study is a contribution to the field of research in the language used in advertising. In this research, the effectiveness of strategic man

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