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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
Wed Sep 01 2021
Journal Name
Journal Of Applied Mathematics
The Dynamics of a Tritrophic Leslie-Gower Food-Web System with the Effect of Fear
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The avoidance strategy of prey to predation and the predation strategy for predators are important topics in evolutionary biology. Both prey and predators adjust their behaviors in order to obtain the maximal benefits and to raise their biomass for each. Therefore, this paper is aimed at studying the impact of prey’s fear and group defense against predation on the dynamics of the food-web model. Consequently, in this paper, a mathematical model that describes a tritrophic Leslie-Gower food-web system is formulated. Sokol-Howell type of function response is adapted to describe the predation process due to the prey’s group defensive capability. The effects of fear due to the predation process are considered in the first two levels

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Publication Date
Sat Jan 01 2022
Journal Name
International Journal Of Clinical Dentistry
THE EFFECT OF A PROTECTIVE BARRIER ON THE SHEAR BOND STRENGTH OF DIFFERENT ORTHODONTIC BRACKETS
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Background and objectives: This study aimed at testing the effect of plastic sleeve or barrier, used to cover the guide of the light cure unit to prevent cross-infection, on the shear bond strength and site of bond failure of stainless steel and ceramic orthodontic brackets. Materials and methods: Forty orthodontic brackets; twenty stainless steel and twenty ceramic brackets bonded to forty extracted human maxillary first premolars using light cure adhesive cured with and without the use of a protective plastic barrier on the guide. Comparing the effect of this barrier on the shear bond strength and adhesive remnant index was performed using an independent t-test and Chi-square test. Results: The protective barrier had decreased the shear b

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Publication Date
Fri Sep 01 2023
Journal Name
Iklīl For Humanities Studies
The Decline of Language Loyalty in the Age of Audiovisual Nearness: A Socio-linguistic Approach
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This article investigates the decline of language loyalty in the age of audiovisual nearness. It is a socio-linguistic review of previous literature related to language disloyalty. It reviews the current theoretical efforts on the impact of audiovisual nearness created by social media and language loyalty. The descriptive design is used. The argument behind this review is that the audiovisual nearness provided by social media negatively affects language loyalty. This article concludes that the current theoretical efforts have paid much attention to the relationship between the audiovisual nearness and language loyalty. Such efforts have highlighted the fact that the social media platforms have provided unprecedented nearness that provoke in

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Computer And Communications
Parallel Quick Search Algorithm for the Exact String Matching Problem Using OpenMP
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String matching is seen as one of the essential problems in computer science. A variety of computer applications provide the string matching service for their end users. The remarkable boost in the number of data that is created and kept by modern computational devices influences researchers to obtain even more powerful methods for coping with this problem. In this research, the Quick Search string matching algorithm are adopted to be implemented under the multi-core environment using OpenMP directive which can be employed to reduce the overall execution time of the program. English text, Proteins and DNA data types are utilized to examine the effect of parallelization and implementation of Quick Search string matching algorithm on multi-co

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Publication Date
Tue Mar 01 2022
Journal Name
The International Journal Of Nonlinear Analysis And Applications
Improved optimality checkpoint for decision making by using the sub-triangular form
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Decision-making in Operations Research is the main point in various studies in our real-life applications. However, these different studies focus on this topic. One drawback some of their studies are restricted and have not addressed the nature of values in terms of imprecise data (ID). This paper thus deals with two contributions. First, decreasing the total costs by classifying subsets of costs. Second, improving the optimality solution by the Hungarian assignment approach. This newly proposed method is called fuzzy sub-Triangular form (FS-TF) under ID. The results obtained are exquisite as compared with previous methods including, robust ranking technique, arithmetic operations, magnitude ranking method and centroid ranking method. This

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
STUDY OF TEMPERATURE EFFECT ON THE HARDNESS FOR EPOXY RESIN AND UNSATURATED POLYESTER
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This search aim to measure Hardness for Epoxy resin and for unsaturated Polyester resin as base materials for composite Hybrid and the materials used is Hybrid fiber Carbon-Kevlar. The Hand Lay-up method was used to manufacture plates of Epoxy resin (EP) and unsaturated Polyester EP,UPE backed by Hybrid fiber (Carbon-Kevlar) and with small volume fraction 5,10 and 15 for every there are Layer of fibers (1,2 and 3). The hardness test was count for material EP, UPE resin and there composites and that we notice that the Hardness (HB) decreased with increase of temperatures.

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Publication Date
Sat May 08 2021
Journal Name
Social Science And Humanities Journal
The impact of accounting for material flow costs in reducing costs: Exploratory study
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Rapid and continuous developments and changes in the modern business environment in all areas of economic, environmental, social, technology and communications push economic units to search for modern methods and methodologies to produce products at low cost as well as produce products that meet the wishes of customers in terms of quality and environment to maintain their market position, and accounting for the costs of the flow of materials is one of the most prominent environmental management accounting techniques capable of providing information to help produce

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Publication Date
Thu Jan 25 2024
Journal Name
Iraqi Journal Of Agricultural Sciences
ECONOMIC FEASIBILITY STUDY FOR THE PROJECT OF CULTURED BARLEY PRODUCTION WITH HYDROPONIC METHOD
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The objective of this research is to know the economic feasibility of hydroponics technology by estimating the expected demand for green forage for the years 2021-2031 as well as Identify and analyze project data and information in a way that helps the investor make the appropriate investment decision in addition to preparing a detailed technical preliminary study for the cultivar barley project focusing on the commercial and financing aspects and the criteria that take into account the risks and uncertainties . that indicating the economic feasibility of the project to produce green forage using hydroponics technology. Cultured barley as a product falls within the blue ocean strategy. Accordingly, the research recommends the necess

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Publication Date
Tue Jan 01 2019
Journal Name
Aip Conference Proceedings
Fabricating and study effect of the concentrations electrolyte for an alkaline electrolysis cell
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Publication Date
Thu Oct 31 2013
Journal Name
Al-khwarizmi Engineering Journal
Simulation of a Wet Sulfuric Acid Process (WSA) for Utilization of Acid Gas Separated from Omani Natural Gas
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In this study, a proposed process for the utilization of hydrogen sulphide separated with other gases from omani natural gas for the production of sulphuric acid by wet sulphuric acid process (WSA) was studied. The processwas simulated at an acid gas feed flow of   5000 m3/hr using Aspen ONE- V7.1-HYSYS software. A sensitivity analysis was conducted to determine the optimum conditions for the operation of plant. This included primarily the threepacked bed reactors connected in series for the production of sulphur trioxidewhich represented the bottleneck of the process. The optimum feed temperature  and catalyst bed volume for each reactor were estimated and then used in the simulation of the whole process for tw

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