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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 Mar 01 2015
Journal Name
Baghdad Science Journal
A study of adsorption isotherms for the removal of herbicide Atlantis WG from aqueous solutions by using Bentonite clay
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The subject of this research involves studying adsorption to removal herbicide Atlantis WG from aqueous solutions by bentonite clay. The equilibrium concentration have been determined spectra photometry by using UV-Vis spectrophotometer. The experimental equilibrium sorption data were analyzed by two widely, Langmuir and Freundlish isotherm models. The Langmuir model gave a better fit than Freundlich model The adsorption amount of (Atlantis WG) increased when the temperature and pH decreased. The thermodynamic parameters like ?G, ?H, and ?S have been calculated from the effect of temperature on adsorption process, is exothermic. The kinetic of adsorption process was studied depending on Lagergren ,Morris ? Weber and Rauschenberg equati

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Publication Date
Tue May 16 2023
Journal Name
Political Sciences Journal
Institutional Reality Construction: Principles of its Construction and Functions of Language in its Production; Diplomacy as a Model
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This study aims to answer a significant problem of social sciences and philosophy: How do we construct an institutional reality such as diplomacy with an objective recognizable existence? The study assumes that the ability to build institutional reality is based on our biological capacity, as it takes different forms in all the institutions we construct. The study takes the theory of the American philosopher John Searle as an approach to examining the assumption. The study sums up important findings; cultures, although they share the biological capacity on which they produce institutional realities, differ in the form of the value standards on which the institutional realities are based. The study recommends the need of Arab social resea

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Publication Date
Mon Oct 06 2025
Journal Name
International Journal Of Innovative Research And Scientific Studies
The requirements of total quality management and the determinants of its application in private Iraqi press institutions: Al-zaman newspaper as a model
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This study investigates the requirements of total quality management (TQM) and the determinants affecting its application in Al-Zaman newspaper, one of Iraq’s leading private press institutions. The research employed a survey methodology, using a structured questionnaire administered to 30 participants representing journalistic, administrative, and technical staff. Five TQM dimensions, each measured through four indicators, were assessed to capture the perceptions of employees regarding the availability and effectiveness of quality practices. Data were analyzed using the Statistical Package for the Social Sciences (SPSS). The results revealed that while senior management at Al-Zaman demonstrates formal support for TQM, there is a

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Publication Date
Fri Jul 27 2012
Journal Name
Journal Of Prosthodontics
A Three-Dimensional Finite Element Analysis for Overdenture Attachments Supported by Teeth and/or Mini Dental Implants
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Publication Date
Fri Jan 01 2021
Journal Name
Systematic Reviews In Pharmacy
A COMPARATIVE STUDY OF CHEMICAL COMPOUNDS AND ANTI-BACTERIAL EFFICACY OF DIFFERENT ALLIUM CEPA PLANT EXTRACTS
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Publication Date
Fri Dec 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
The Influence of Different Fabrication and Impression Techniques on the Marginal Adaptation of Lithium Disilicate Crowns (A comparative in vitro study)
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Background: The marginal adaptation has a key role in the success and longevity of the fixed dental restoration, which is affected by the impression and the fabrication techniques .The objective of this in vitro study was to evaluate and compare the marginal fitness of lithium disilicate crowns using two different digital impression techniques (direct and indirect techniques) and two different fabrication techniques (CAD/CAM and Press techniques). Materials and Methods: Thirty two sound upper first premolar teeth of comparable size extracted for orthodontic reason were selected in this study .Standardized preparation of all teeth samples were carried out with modified dental surveyor to receive all ceramic crown restoration with 1 mm deep

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Publication Date
Sat Nov 15 2025
Journal Name
Journal Of Legal Sciences
A comparative study between the federal investment law No. 13 of 2006 and the Investment Law Kurdistan No. 4 of 2006
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Publication Date
Thu Sep 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
360 degree reverse feedback / comparative analytical study for a sample of managers and heads of departments in the Central Electricity DepartmentAnd the General Directorate of Water and Sewage
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يسعى البحث إلى الاهتمام بإحدى الوظائف المهمة في إدارة الموارد البشرية وهي تقويم الأداء التي تواجه مجموعة من الانتقادات والآراء السلبية، اذ ظهر في الأّونة الأخيرة أنموذج جديد يمكن إن يتجاوز تلك السلبيات وهو أنموذج التغذية العكسية المتعدد المصادر درجة .وقد حاول الباحثان توظيف هذا المفهوم في اثنتين من المنظمات العامة العراقية هما (دائرة كهرباء الوسط) التابعة لوزارة الكهرباء
و (دائرة الماء والمجاري) ال

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Publication Date
Sat Jan 01 2022
Journal Name
Revista Iberoamericana De Psicologia Del Ejercicio Y El Deporte
THE EFFECT OF A PROPOSED TRAINING PROGRAM USING INTERMITTENT TRAINING TO DEVELOP SOME PHYSICAL AND BIO-KINEMATIC VARIABLES AND ACCURACY OF THE JUMP SPIKE SERVE SKILL IN VOLLEYBALL
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The purpose of this paper is to identifying the values of some physical and Bio- Kinematic variables during the performance of the jump spike serve skill, and identifying the effect of the proposed training program using intermittent training to develop some physical and Bio- Kinematic variables and accuracy of the jump spike serve skill among the research sample. The experimental method was used and the research was conducted on a deliberately chosen sample of the players of the Army Club, who were primarily advanced in volleyball, and the number of the sample was (10) players. The conclusions were reached that the proposed training program using intermittent training has a positive effect on some of the physical and Bio- Kinematic variabl

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Publication Date
Sat Nov 15 2025
Journal Name
Mustansiriya Medical Journal
The Pattern Of Skin Diseases Among Kindergarten Children In Baghdad. A Comparative Study Between Two Surveys Five Years Apart
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