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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 Jan 24 2016
Journal Name
Al-academy
Experimentation in caves painting (A comparative analysis): فريد خالد علوان
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Addressed the problem of the research is marked (experimentation in caves fee) concept and its role in experimentation deviate Display Num formal charges caves. The search came in four sections: general framework for research and identified the research problem and the need for him. With an indication of the importance of his presence. Then specify the search for the goals of (revealed the nature and role of experimentation in determining the nature of Manifesting fee documented on the walls of caves), followed by the establishment of the three search limits (objectivity, the temporal and spatial) were then determine the terms related to the title. Then provide the theoretical framework and indicators that resulted from academic theorizi

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Advanced Pharmacy Education And Research
Comparative biosimilar quality studies between a rituximab product and MabThera
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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
Determination of the neutron refleetion coefficient as a function of reflector material
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This work presents a simple method for determination of the neutron reflection coefficient (n) as a function of different neutron reflector materials.A laboratory neutron source (Am-Be) with activity of 16 ci is employed with a (BF3) neutron detector. Am-BeThree types of reflector materials are used as samples, the thickness of each sample is (5cm).It is found that( ?7) is: -For polyethlyene = 0.818

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Publication Date
Mon Oct 22 2018
Journal Name
Journal Of Economics And Administrative Sciences
The challenges facing the Insurance sector in Iraq Analytical study in Iraqi insurance companies (National insurance company as model)
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Most of World nations are striving to provide the necessary needs to protect their economic properties assets against natural or abnormal disasters that may be inflicted on such property and the means that used by such countries to reduce the damages is insurance, whereas insurance as a system that collects and distributes different risks into the group thus  to achieve a social symbiosis between individuals. The system works to transfer the risks from the individual to the group and then distributes the losses to all members of the group.

According to the importance of the insurance sector and the need to develop it as well as working on improving its performance, this search aims to identify the ac

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Publication Date
Wed Jun 07 2023
Journal Name
Journal Of Educational And Psychological Researches
Multiple Intelligence Test Item Selection-Based on Howard Gardner's MI Model Using a Generalized Partial Estimation Model: Ministry of Education \ Karkh First Directorate of Education
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The aim of the research is to examine the multiple intelligence test item selection based on Howard Gardner's MI model using the Generalized Partial Estimation Form, generalized intelligence. The researcher adopted the scale of multiple intelligences by Kardner, it consists of (102) items with eight sub-scales. The sample consisted of (550) students from Baghdad universities, Technology University, al-Mustansiriyah university, and Iraqi University for the academic year (2019/2020). It was verified assumptions theory response to a single (one-dimensional, local autonomy, the curve of individual characteristics, speed factor and application), and analysis of the data according to specimen partial appreciation of the generalized, and limits

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Publication Date
Sun Mar 04 2018
Journal Name
Journal Of The College Of Education For Women
Novel of (Ya Mariam), for Sinan Antwane : A Pragmatic Study
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Pragmatics looked at literary discourse as an external subject that needed an actor and based on a communicative relationship, that is, it examines literary work by focusing on the author's intent, and attempting to monitor the pilgrim and logical dimension in the text. It focuses on the practical and communicative aspect of the language, which aims to convince the recipient and his or her emotional influence.And the novel (Yamrim) starting from the title (Sos) communication, and building dialogue and pilgrims based on two different logic completely, the logic of optimism and look at things with absolute objectivity, the logic of pessimism and closure and look at things with absolute passion. These two tendencies are embodied by the char

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Publication Date
Fri Jun 27 2025
Journal Name
Journal Of Al-turath University College
Implications of the political responsibility of the government (Comparative study)
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Publication Date
Mon Jul 18 2022
Journal Name
International Journal Of Early Childhood Special Education
The effectiveness of a proposed teaching strategy according to The Common Knowledge Construction Model in Mathematical Proficiency for middle school student
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This research aims to know the effectiveness of teaching with a proposed strategy according to the common Knowledge construction modelin mathematical proficiency among students of the second middle class. The researchers adopted the method of the experimental approach, as the experimental design was used for two independent and equal groups with a post-test. The experiment was applied to a sample consisting of (83) students divided into two groups: an experimental comprising (42) students and a control group, the second comprising (41) students., from Badr Shaker Al-Sayyab Intermediate School for Boys, for the first semester of the academic year (2021-2022), the two groups were rewarded in four variables: (chronological age calculated in mo

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Publication Date
Tue Sep 01 2015
Journal Name
Journal Of Engineering
Cost of Optimum Design of Trunk Mains Network Using Geographical Information System and Support Programs
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Sewer network is one of the important utilities in modern cities which discharge the sewage from all facilities. The increase of population numbers consequently leads to the increase in water consumption; hence waste water generation. Sewer networks work is very expensive and need to be designed accurately. Thus construction effective sewer network system with minimum cost is very necessary to handle waste water generation.

 In this study trunk mains networks design was applied which connect the pump stations together by underground pipes for too long distances. They usually have large diameters with varying depths which consequently need excavations and gathering from pump stations and transport the sewage

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Publication Date
Fri Mar 31 2017
Journal Name
Journal Of Engineering
Cultivation of Chlorella Vulgaris Using Airlift Photobioreactor Sparged with 5%CO 2 -Air as a Biofixing Process
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The present paper addresses cultivation of Chlorella vulgaris microalgae using airlift photobioreactor that sparged with 5% CO 2 /air. The experimental data were compared with that obtained from bioreactor aerated with air and unsparged bioreactor. The results showed that the concentration of biomass is 0.36 g l -1  in sparged bioreactor with CO2/air, while, the concentration of biomass reached to 0.069 g l -1  in the unsparged bioreactor. They showed also that aerated  ioreactor.with CO2/air gives more biomass production even the bioreactor was aerated with air. This study proved that application of sparging system for  ultivation of Chlorella vulgaris microalgae using either CO2/air mixture or air has a significant

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