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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 Mar 10 2021
Journal Name
Baghdad Science Journal
Newly Developed System For The Analysis Of Micro Quantites Of Molybdenum (VI) Using Flow Injection Analysis
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New microphotometer was constructed in our Laboratory Which deals with the determination of Molybdenum (VI) through its Catalysis effect on Hydrogen peroxide and potasum iodide Reaction in acid medium H2SO4 0.01 mM. Linearity of 97.3% for the range 5- 100 ppm. The repeatability of result was better than 0.8 % 0.5 ppm was obtanined as L.U. (The method applied for the determination of Molybdenum (VI) in medicinal Sample (centrum). The determination was compared well with the developed method the conventional method.

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Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of weighted estimated method and proposed method (BEMW) for estimation of semi-parametric model under incomplete data
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Generally, statistical methods are used in various fields of science, especially in the research field, in which Statistical analysis is carried out by adopting several techniques, according to the nature of the study and its objectives. One of these techniques is building statistical models, which is done through regression models. This technique is considered one of the most important statistical methods for studying the relationship between a dependent variable, also called (the response variable) and the other variables, called covariate variables. This research describes the estimation of the partial linear regression model, as well as the estimation of the “missing at random” values (MAR). Regarding the

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Publication Date
Thu Dec 03 2015
Journal Name
Journal Of New Theory
TOPOLOGY SPECTRUM OF A KU-ALGEBRA
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The aim of this paper is to study the Zariski topology of a commutative KU-algebra. Firstly, we introduce new concepts of a KU-algebra, such as KU-lattice, involutory ideal and prime ideal and investigate some basic properties of these concepts. Secondly, the notion of the topology spectrum of a commutative KU-algebra is studied and several properties of this topology are provided. Also, we study the continuous map of this topological space.

Publication Date
Mon Oct 01 2012
Journal Name
2012 Ieee International Conference On Circuits And Systems (iccas)
A survey of on-chip monitors
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Systems on Chips (SoCs) architecture complexity is result of integrating a large numbers of cores in a single chip. The approaches should address the systems particular challenges such as reliability, performance, and power constraints. Monitoring became a necessary part for testing, debugging and performance evaluations of SoCs at run time, as On-chip monitoring is employed to provide environmental information, such as temperature, voltage, and error data. Real-time system validation is done by exploiting the monitoring to determine the proper operation of a system within the designed parameters. The paper explains the common monitoring operations in SoCs, showing the functionality of thermal, voltage and soft error monitors. The different

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Publication Date
Sun Mar 26 2023
Journal Name
Wasit Journal Of Pure Sciences
Pure Graph of a Commutative Ring
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A new definition of a graph called Pure graph of a ring denote Pur(R) was presented , where the vertices of the graph represent the elements of R such that there is an edge between the two vertices ???? and ???? if and only if ????=???????? ???????? ????=????????, denoted by pur(R) . In this work we studied some new properties of pur(R) finally we defined the complement of pur(R) and studied some of it is properties

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Publication Date
Tue Dec 01 2020
Journal Name
Baghdad Science Journal
A Generalization of t-Practical Numbers
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This paper generalizes and improves the results of Margenstren, by proving that the number of -practical numbers  which is defined by   has a lower bound in terms of . This bound is more sharper than Mangenstern bound when  Further general results are given for the existence of -practical numbers, by proving that the interval contains a -practical for all

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Publication Date
Wed Feb 01 2023
Journal Name
Baghdad Science Journal
Order Sum Graph of a Group
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The concept of the order sum graph associated with a finite group based on the order of the group and order of group elements is introduced. Some of the properties and characteristics such as size, chromatic number, domination number, diameter, circumference, independence number, clique number, vertex connectivity, spectra, and Laplacian spectra of the order sum graph are determined. Characterizations of the order sum graph to be complete, perfect, etc. are also obtained.

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Publication Date
Wed Aug 29 2018
Journal Name
Journal Of Engineering
Exergy Analysis of a Domestic Refrigerator
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An energy and exergy thermodynamic analysis using EES program was done for a domestic refrigerator working with R-134a using vapor compression refrigeration cycle. The analysis deals with the system component, i.e. compressor, condenser, evaporator and the expansion device. The analysis depends on the entropy generation minimization approach to improve the refrigerator performance by exploring the optimum design points. These design points were derived from three different theories governing the entropy generation minimization using exergy analyzing method. These theories were first applied to find the optimum balance between the hot inner condenser area and the cold inner evaporator area of the refrigerator and between

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Publication Date
Mon Oct 30 2023
Journal Name
Journal Of Discrete Mathematical Sciences & Cryptography
Associate graph of a commutative ring
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In this study, a brand-new graph definition known Associate graph of a ring R denote Ass(R) is present, where the graph’s vertices stand in for R’s elements s.t, any two vertices α and β  merage by an edge if and only if α = rβ and β = sα. In this paper, we investigated some new property of Ass (R)  are studied., the complement of Ass (R) is finally defined and a few of its characteristics are researched.

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Publication Date
Sun Aug 01 2021
Journal Name
Materials Today: Proceedings
A review of automatic history matching
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