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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
Mon Jun 30 2025
Journal Name
International Journal Of Sustainable Development And Planning
The Role of Sustainable Environmental Indicators in Urban Happiness: A Study of Al-Amir Neighborhood in Al-Najaf City, Iraq
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Publication Date
Mon May 01 2023
Journal Name
Environmental Nanotechnology, Monitoring & Management
A review study summarizes the main characterization techniques of nano-composite photocatalysts and their applications in photodegradation of organic pollutants
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Publication Date
Wed Feb 21 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Perceptions of Senior Pharmacy Students Towards the Impact of Artificial Intelligence on University Education and Scientific Writing: A Qualitative Study
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Background: The roles of AI in the academic community continue to grow, especially in the enhancement of learning outcomes and the improvement of writing quality and efficiency. Objectives: To explore in depth the experience of senior pharmacy students in using artificial intelligence for academic purposes. Methods: This qualitative study included face-to-face individual interviews with senior pharmacy students from March to May 2023 using a pre-planned interview guide of open-ended questions. All interviews were audio-recorded. Thematic analysis was used to analyze the data. Results: The results were obtained from 15 in-depth face-to-face interviews with senior pharmacy students (5th and 4th years). Eight participants were male, and seven

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Publication Date
Wed Feb 21 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Perceptions of Senior Pharmacy Students Towards the Impact of Artificial Intelligence on University Education and Scientific Writing: A Qualitative Study
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Background: The roles of AI in the academic community continue to grow, especially in the enhancement of learning outcomes and the improvement of writing quality and efficiency. Objectives: To explore in depth the experience of senior pharmacy students in using artificial intelligence for academic purposes. Methods: This qualitative study included face-to-face individual interviews with senior pharmacy students from March to May 2023 using a pre-planned interview guide of open-ended questions. All interviews were audio-recorded. Thematic analysis was used to analyze the data. Results: The results were obtained from 15 in-depth face-to-face interviews with senior pharmacy students (5th and 4th years). Eight participants were male, an

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Publication Date
Mon Jan 02 2017
Journal Name
Al-academy
Structural elements of composition design for fabrics image Image footage model
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End of the twentieth century witnessed by the technological evolution Convergences between the visual arts aesthetic value and objective representation of the image in the composition of the design of the fabric of new insights and unconventional potential in atypical employment. It is through access to the designs of modern fabrics that address the employment picture footage included several scenes footage from the film, which focuses on research and analytical as a study to demonstrate the elements of the picture and the organization of its rules and how to functioning in the design of fabrics, Thus, it has identified the problem by asking the following: What are the elements of the picture footage and how the functioning of the struct

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Publication Date
Wed Jun 01 2022
Journal Name
Bulletin Of Electrical Engineering And Informatics
Proposed model for data protection in information systems of government institutions
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Information systems and data exchange between government institutions are growing rapidly around the world, and with it, the threats to information within government departments are growing. In recent years, research into the development and construction of secure information systems in government institutions seems to be very effective. Based on information system principles, this study proposes a model for providing and evaluating security for all of the departments of government institutions. The requirements of any information system begin with the organization's surroundings and objectives. Most prior techniques did not take into account the organizational component on which the information system runs, despite the relevance of

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Publication Date
Thu Mar 19 2015
Journal Name
Al-academy
Theatrical Visual System between the Cultural Identity and Globalization Culture Iraqi Theatre as Case Study
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Publication Date
Wed Sep 01 2021
Journal Name
Baghdad Science Journal
Biochemical and Histological Study of Aminoacylase-1 Purified from Amniotic Fluid in Rats with Oxidative Stress Induced by Lead Acetate
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This work involves separating and studying the aminoacylase-1 (ACY1) of amniotic fluid from healthy pregnant, mainly one peak with higher activity has been isolated by DEAE-Cellulose ion exchange from the proteinous supernatant produced by deposition of proteins using ammonium sulfate  (65%) after dialysis. The purification folds reaching to 19 folds also gave one protein peak when injected into the gel filtration column, a high ACY1 purity was obtained, with 38 folds of purification. It was found that the molecular weight of the isolated ACY1 was up to 46698 Dalton when using gel chromatography technique.The effect of ACY1 isolate was studied on rats with oxidative stress caused by lead acetate(LA) at 40 mg / kg body weight and compare

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Publication Date
Sat Aug 31 2024
Journal Name
International Journal Of Intelligent Engineering And Systems
Credit Card Fraud Detection Using an Autoencoder Model with New Loss Function
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Solving Time-Cost Tradeoff Problem with Resource Constraint Using Fuzzy Mathematical Model
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Scheduling considered being one of the most fundamental and essential bases of the project management. Several methods are used for project scheduling such as CPM, PERT and GERT. Since too many uncertainties are involved in methods for estimating the duration and cost of activities, these methods lack the capability of modeling practical projects. Although schedules can be developed for construction projects at early stage, there is always a possibility for unexpected material or technical shortages during construction stage. The objective of this research is to build a fuzzy mathematical model including time cost tradeoff and resource constraints analysis to be applied concurrently. The proposed model has been formulated using fuzzy the

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