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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
Fri Sep 01 2023
Journal Name
Journal Of Molecular Structure
Synthesis, spectral studies, DFT, biological evaluation, molecular docking and dyeing performance of 1-(4-((2-amino-5-methoxy)diazenyl)phenyl) ethanone complexes with some metallic ions
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Publication Date
Sun Jul 17 2022
Journal Name
Al–bahith Al–a'alami
Post-interactive communication A study to build a model for the flow of communication in social networking sites
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The issue of the research lies in the non-representation of the models developed for the communication process in the interaction and networking processes through social media, as the research sought to build a network model of communication according to the specific data and features of social media platforms in order to reach a special generalization to understand how the process of networking operates in cyberspace.

The researcher followed the analytical survey approach as she described the communication models outwardly in order to be able to build a networked communication model that represents the flow of post-reactive communication. Therefore, it has been named "Nebula - Sadeem" after the concept of post-space and cosmic g

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Publication Date
Wed Mar 01 2023
Journal Name
International Journal Of Research In Social Sciences And Humanities
The Role of Value Chain Analysis as well as Programs and Performance Budget in Reducing Waste of Public Money(Applied Study)
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Programs and performance budget represents a sophisticated method of public budget numbers, which includes all allocations to be determined for each job or activity within a government entity, which is analyzed according to their needs and costs, and this method can be applied using one of the cost accounting techniques, which is the technique of analyzing the value chain that reduces costs by avoiding activities that do not add value and enhance activities that add value to the economic entity, the current research aims to develop the budget system in government entity by using the budget of programs and performance as a tool for planning and monitoring events and activities, thereby reducing the waste of public money by reducing unnecessa

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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 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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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
Wed Jun 01 2016
Journal Name
Journal Of Engineering
Accuracy Evaluation of Digital Elevation Model Created Using Handheld Global Positioning System Receivers
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This study aims to assess the accuracy of digital elevation model (DEM) created with utilization of handheld Global Positioning System (GPS) and comparing with Advanced Spaceborne Thermal Emission and Reflection Radiometer Global Digital Elevation Model (ASTER GDEM), version 2. It is known that the quality of the DEM is affected by both of accuracy of elevation at each pixel (absolute accuracy) and accuracy of presented morphology (relative accuracy). The University of Baghdad, Al Jadriya campus was selected as a study area to create and analysis the resulting DEM. Additionally, Geographic Information System (GIS) was used to visualize, analyses and interpolate GPS track points (elevation data) of the study area. In this

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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
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
Sat May 27 2017
Journal Name
Journal Of Pharmaceutical Sciences And Research
Synthesis, Preliminary Antimicrobial Evaluation and Molecular Docking of new Schiff bases of Ceftizoxime
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Schiff bases of Ceftizoxime sodium were synthesized in an attempt to improve the antimicrobial spectrum of Ceftizoxime. Aminothiazole ring of Ceftizoxime is linked directly through an imino group to different aromatic aldehydes reacted by nucleophilic addition using trimethylamine (TEA), as a catalyst and refluxed in methanol. The antimicrobial activity was evaluated for such Schiff bases using disc diffusion method. Molecular docking was conducted on certain penicillin-binding proteins (PBPs) and carboxypeptidases using 1- click docking software. Schiff bases of Ceftizoxime were prepared with reasonable yields and their chemical structures were confirmed by spectral analysis (FTIR, 1H-NMR) and elemental microanalysis (CHNS). The antibacter

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