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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 Apr 30 2019
Journal Name
International Journal Of Environmental Research
A Comparative Study for the Identification of Superior Biomass Facilitating Biosorption of Copper and Lead Ions: A Single Alga or a Mixture of Algae
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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Developing Human Capital according to the Communities of Practice: A comparative study by using Data Envelopment Analysis
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The research discusses the need to find the innovative structures and methodologies for developing Human Capital (HC) in Iraqi Universities. One of the most important of these structures is Communities of Practice (CoPs) which contributes to develop HC by using learning, teaching and training through the conversion speed of knowledge and creativity into practice. This research has been used the comparative approach through employing the methodology of Data Envelopment Analysis (DEA) by using (Excel 2010 - Solver) as a field evidence to prove the role of CoPs in developing HC. In light of the given information, a researcher adopted on an archived preliminary data about (23) colleges at Mosul University as a deliberate sample for t

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Publication Date
Thu Sep 23 2021
Journal Name
Egyptian Journal Of Chemistry
Some 3,4,5-Trisubstituted-1,2,4-triazole Synthesis, Antimicrobial Activity, and Molecular Docking Studies
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Publication Date
Wed Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Development and in vitro Evaluation of Bioadhesive Vaginal Tablet using Econazole Nitrate as a Model Drug
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         In this study, a bioadhesive dosage form of eoconazole nitrate for vaginal delivery was designed using a combination of bioadhesive polymers: Carbopol 941 p and sodium carboxymethylcellulose or methylcellulose in different ratios. The bioadhesive strength was evaluated by measuring the force required to detach the tablet from sheep vaginal mucosal membrane. It was found that the bioadhesive force was directly proportional to Carbopol 941 p content in the different formulae. The formulae were tested for their swelling behavior using agar gel plate method. The results showed that formulae containing a combination of Carbopol 941 p and sodium carboxymethylcellulose had greater swelling index

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Publication Date
Tue Jan 01 2019
Journal Name
Indian Journal Of Public Health Research & Development
Comparative Study of Hepcidin and Some Inflammatory Parameters in Pregnant Women at the Three Trimesters
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Publication Date
Mon Jun 30 2003
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Study of the Drying of Ethanol using Zeolite Molecular Sieves
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Publication Date
Fri May 31 2019
Journal Name
Journal Of Engineering
A Comparative Study of Various Intelligent Algorithms based Path Planning for Mobile Robots
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In general, path-planning problem is one of most important task in the field of robotics. This paper describes the path-planning problem of mobile robot based on various metaheuristic algorithms. The suitable collision free path of a robot must satisfies certain optimization criteria such as feasibility, minimum path length, safety and smoothness and so on. In this research, various three approaches namely, PSO, Firefly and proposed hybrid FFCPSO are applied in static, known environment to solve the global path-planning problem in three cases. The first case used single mobile robot, the second case used three independent mobile robots and the third case applied three follow up mobile robot.  Simulation results, whi

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Publication Date
Sun Jul 20 2025
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Using a 3D Chaotic Dynamic System as a Random Key Generator for Image Steganography
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In today's digital era, the importance of securing information has reached critical levels. Steganography is one of the methods used for this purpose by hiding sensitive data within other files. This study introduces an approach utilizing a chaotic dynamic system as a random key generator, governing both the selection of hiding locations within an image and the amount of data concealed in each location. The security of the steganography approach is considerably improved by using this random procedure. A 3D dynamic system with nine parameters influencing its behavior was carefully chosen. For each parameter, suitable interval values were determined to guarantee the system's chaotic behavior. Analysis of chaotic performance is given using the

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Publication Date
Wed May 24 2023
Journal Name
2023 9th International Conference On Information Technology Trends (itt)
A Comparative Study of Unauthorized Drone Detection Techniques
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Publication Date
Tue Aug 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Post a reflection on the capabilities of personnel programs A prospective study of a sample of the views of the staff at the Ministry of Higher Education and Scientific Research
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            This research aims to know the role and impact of participation in the capabilities of human resources programs, and for the purpose of measuring it has been determined the dimensions of these two variables by relying on standards for this purpose, was chosen as the Ministry of Higher Education and Scientific Research / device supervision and scientific calendar as one of the important departments in the ministry and includes a large number of individuals at different organizational levels for the purpose of answering a questionnaire prepared for the purpose of measurement and access to the results and the achievement of the objectives of the research and which ha

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