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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 31 2024
Journal Name
مـجـلــة الـدراســات التربــويــة والعـلـمـيــة - كلـيــة الـتــربـيــة - الجــامـعـة العـراقـيــة ال
Synthesis, Characterization and Studies on Thermal, Antioxidant, Docking and Biological of New Ligands with Some Metal Complexes
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Publication Date
Fri May 15 2009
Journal Name
Journal Of Planner And Development
Study of Change in Regional Land Use Using Remote Sensing Technology and Geographic Information Systems / Study Area (Hawr Al Huweiza) for the Years 1973-1990-2004
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his project try to explain the using ability of spatial techniques for land cover change detection on regional level with the time parameter and did select for explain these abilities study case (Hewaizah marsh ) . this area apply to many big changes with the time. These changes made action on characters and behaviors of this area as well as all activities in it . This Project concerting to recognize the Using importance of remote sensing and GIS Methodology in data collecting for the changes of land use and the methodology for the analyses and getting the results for the next using as a base data for development and drawing the plans as well as in regional planning .This project focus on practical

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Publication Date
Sat Mar 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The use of technology review and evaluate programs PERT to improve the cost method on the basis of activity: بحث تطبيقي في الشركة العامة للصناعات النسيجية /واسط
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Suffer most of the industrial sector companies from high Kperfi magnitude of the costs of industrial indirect, lack of equitable distribution of these costs on the objectives of cost, increased competition, and the lack of proper planning in line and changes faced by the industrial sector (general) and sample (private), as well as the difficulty in re- directing efforts to improve profitability and in-depth analysis of activities, and to identify untapped resource activities, then link these activities to the final products  The research aims to apply the technology review and evaluate programs with the method (ABC) through the application stages of planning, scheduling and control and a comparison to get to the products of dev

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Publication Date
Wed May 15 2024
Journal Name
International Journal Of Religion
(The Importance of Knowledge and Work in Islamic Thought) A Study of the Stages of Spiritual Purification According to Imam Al-Ghazali
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Science occupies great importance in Islamic thought. Science and learning are considered an essential part of Islamic teachings, and this importance appears in several aspects,Among them is thatScience as a means of understanding religion :Science is a means of understanding the teachings of the Islamic religion. Islam encourages thinking and rational research to understand the Holy Quran and the Sunnah of the Prophet, enabling Muslims to direct their lives and actions in accordance with the directives of their religion,And also to encourageResearch :Islam encourages scientific research and the use of reason in understanding the nature of the universe and God’s signs in it. Muslims are encouraged to study the natural and social s

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Strategic orientation and its reflection on the Learning organization: Survey study of a sample of Makers decision the Iraqi Ministry of Communications
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The current research focuses on the extent to which the strategic orientation(entrepreneurial orientation, customer orientation, technology orientation, learning orientation, and investment orientation) affects the learning organization (building common vision, systemic thinking, personal dominance, mental models, team learning)The first hypothesis to test the connection relation between research variables and The second hypothesis was to test the relationship between these variables. In order to ascertain the validity of the hypotheses, the research was based on a questionnaire questionnaire prepared according to a number of In addition to building a fifth sub-variable for the strategic orientation (investment orientation) based

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Publication Date
Sat Jun 06 2020
Journal Name
Journal Of The College Of Education For Women
Spatial Analysis of Soil Characteristics and its Effect on Determining the Susceptibility of lands of the RasheedRegion: A Study in Soil Geography
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Twelve pends were selected and distributed on three verticals transects paths on the Tigers river in Al Rasheed county.Passing through land covers, that classified and covers the whole region. Based on the 8 Landsat of the year 2015. It was oriental classified by using Erdas 10.2 . The pedons were distributed on the area of each varicty of these classes. the series of soil according of the transect series (DW74,MMg,DMu6 , Df96) respectively were represented P1 , P2 , P3 , P4  .

The second transits series(DM97,MM5,DM96,DF115) respectively were  represented P5 , P6 , P7 , P8  .The third  transits series(DM46,MMg,MF12,MM11) re

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The role of marketing recovery in improving the organization's reputation An applied study of a sample of private bank managers in Baghdad
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This research aims to know and the role of the marketing recovery dimensions in improving the organization's reputation through an exploratory study of private banks in the city of Baghdad. The aim of the research is to define the role of the marketing recovery through its dimensions (compensation, apology, speed of response, assistance and problem solving), in improving the organization's reputation, as the research will attempt to provide a theoretical framework for the dimensions studied through the most important of what researchers presented and then conduct the applied aspect of the research. Data were collected using a questionnaire-based survey consisting of 35 questions and distributed to 110 managers of private banks in

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Publication Date
Sat Dec 15 2018
Journal Name
Journal Of Baghdad College Of Dentistry
Clinicopathological and Immunohistochemical Analysis of 21 cases of Traumatic Ulcerative Granuloma with Stromal Eosinophilia Using CD30, CD68 and TGF-β1
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Background: Traumatic ulcerative granuloma with stromal eosinophilia is an impressive benign chronic ulcerative lesion of the oral mucosa with vague etiopathogenesis. It was supposed to represent an oral counterpart of primary cutaneous CD30+ lymphoproliferative disorder. Histopathologically, it is characterized by mixed inflammatory infiltrate predominated by histiocytes, lymphocytes and eosinophils along with presence of scattered large atypical mononuclear cells. It has worrisome clinical presentation. It may heal spontaneously, but in most occasions it persists and never heal unless removed surgically (incisional or excisional biopsy). A rare subset may show worrisome immunohistochemical features. Follow up is highly recommended. Mat

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Publication Date
Fri Dec 30 2011
Journal Name
Mustansiria Dental Journal
Effect of microwave irradiation on disinfection, dimensional accuracy, and surface porosity of dental casts
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To evaluate the effectiveness of different microwave irradiation exposure times on the disinfection of dental stone samples immersed in different solutions, and its affect on the dimensional accuracy and surface porosity. Dental stone casts were inoculated with an isolate of Bacillus subtilis to examine the efficiency of microwave irradiation as a disinfection method while immersed in different solutions; water, 40% sodium chloride, or without immersion for different durations. Dimensional accuracy and surface porosity were also evaluated. Significant reduction in colony counts of Bacillus subtilis were observed after 5 minutes of microwave irradiation of immersed dental casts in water and NaCl solution. No evidence of growth was observed a

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Publication Date
Sun Jun 30 2024
Journal Name
Lark
The Image of the Arab in Hebrew Literature for Young Adults – A Reading of the Novel “Nadia” by Kalila Ron Feder
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يهدف هذا البحث الى التطرق الى صورة العربي كما يعرضها ادب اليافعين العبري في رواية " نادية " للكاتبة العبرية " كاليلا رون فيدر " . والتي تعد من الاديبات العبريات اللواتي تطرقن بصورة مباشرة الى موضوع ما خلف الجدار ، والصراع العربي – الإسرائيلي وانعكاساته على المجتمع الإسرائيلي بصورة عامة والمجتمع العربي بصورة خاصة . ينقسم هذا البحث إلى ثلاثة فصول، تطرق الفصل الأول  إلى "ادب اليافعين"، و تاريخه ، مميزاته والفئ

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