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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
Sun Nov 01 2020
Journal Name
Physics Of Atomic Nuclei
Study of the Halo Structure for Some Light Neutron-Rich Nuclei Using the Cosh Potential
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The radial wave functions of the cosh potential within the three-body model of (Core+ 2n) have been employed to investigate the ground state properties such as the proton, neutron and matter densities and the associated rms radii of neutron-rich 6He, 11Li, 14Be, and 17B exotic nuclei. The density distributions of the core and two valence (halo) neutrons are described by the radial wave functions of the cosh potential. The obtained results provide the halo structure of the above exotic nuclei. Elastic electron scattering form factors of these halo nuclei are studied by the plane-wave Born approximation.

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A model of a proposed audit program to audit the strategies of municipal institutions and its impact on achieving sustainable development: An applied research in the municipal institutions of Karbala Governorate
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Abstract

                  The study aimed to prepare a practical guide for procedures for auditing the strategies of municipal institutions in achieving sustainable development by adopting the idea of ​​the audit matrix through which a classified report is prepared according to the dimensions of sustainable development, by preparing a specialized audit program for the purpose of auditing strategies for achieving sustainable development and emptying the results of the application of each of the paragraphs The program in the audit matrix that was prepared for the purpose of determining the impact of each observation and linkin

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Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
A study of the solvent effect on the low temperature spectra of benzoanthracene molecules
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been taken at room temperature down to liquid nitrogen temperature (77K). Polar and nonpolar solvents have been used to study the solvent effect on the absorption and fluorescence spectra of solute molecules. Some of the spectroscopic parameters have been determined as functions of solvent polarity and temperature. The results indicate that the band width FWHM increases with increasing the solvent polarity and temperature, while the peak emission cross section decreases with increasing of solvent polarity and decreases with increasing the temperatures. Clear vibrational structure spectra of benzoanthracene molecules have been observed in Nonane and Hexane solvents at 77K.

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Requirements of investment in the marsh : a case study in the Marshlands of Maysan
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The search aims to find out the most important requirements for the success of marshes investment and maximize the expected returns of investment was marked by a problem find aquestion for availability requirements necessary for the success of marshes investment has a research community owners decision in the province Maysan the most important conclusions to the search is that the investment great importance in support of the economy and raising the cultural and social level, there is no investment successful but only with configure the investment environment appropriate economic, social, cultural, political, and security ways. the most important recommendations are working on the provision of the investment environment appropria

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Publication Date
Sat Dec 02 2023
Journal Name
Journal Of Engineering
Evaluation of the Stability and Flow of Asphalt Concrete Produced with Waste Brick Tile Powder as a Filler
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The utilization of recycled brick tile powder as a replacement for conventional filler in the asphalt concrete mix has been studied in this research. This research evaluates the effectiveness of recycled brick tile powder and determines its optimum replacement level. Using recycled brick tile powder is significant from an environmental standpoint as it is a waste product from construction activities. Sixteen asphalt concrete samples were produced, and eight were soaked for a day. Samples contained 5% Bitumen, 2% to 5% brick tile powder, and conventional stone dust filler. The properties of samples were evaluated using the Marshall test. It was observed that the resistance to stiffness and deformation of asphalt concrete

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Publication Date
Thu Dec 20 2007
Journal Name
Journal Of Planner And Development
To contribute in handling the housing crisis in the city of BaghdadA study for the decision of the Mayoralty of Baghdad to allow adding a third floor for the residential units
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We need to know the basic facts concerning planning top and bottom limits including any critical levels or the threshold over which the cost would be much higher for land development. Therefore this paper concerned with Baghdad Municipality decision No.2/1004 dated 7/12/2004. The reason behind this decision is the hope to face up at least in the severe housing crisis in the city of Baghdad. This paper attempts to know the attitude of the local community in the general through a field study of people living near such dwelling where third floors are added of. This might indicate any positive or negative effects whether on short or long-term including its effect on the theoretical side including the population growth of Baghdad, the

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Publication Date
Tue Oct 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Solution of Fuzzy Maximal Flow Problems of Vehicles in Province of Diwaniyah Using the Ranking Function for Fuzzy Linear Programming Model
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Abstract

The traffic jams taking place in the cities of the Republic of Iraq in general and the province of Diwaniyah especially, causes return to the large numbers of the modern vehicles that have been imported in the last ten years and the lack of omission for old vehicles in the province, resulting in the accumulation of a large number of vehicles that exceed the capacity of the city's streets, all these reasons combined led to traffic congestion clear at the time of the beginning of work in the morning, So researchers chose local area network of the main roads of the province of Diwaniyah, which is considered the most important in terms of traffic congestion, it was identified  fuzzy numbers for

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Publication Date
Tue Mar 01 2016
Journal Name
Al-academy
Harmonization formative in the design of interior spaces Hall of discussions in the design department (a model): بدريا محمد حسن فرج
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Can not reach a comprehensive concept for interior design through the use of Harmonization term according transformations experienced by the terms of the variables associated with the backlog of cultures that characterize concepts according to the nature of the users of the spaces in the design output, which necessitates the meaning of the combination of knowledge, art, science, such as the type of perceptions design the Harmonization cognitive science with art to create products of the use of design configurations that help the designer to put such a product within the reality and like the fact that reliable, as well as the rational knowledge tend somehow to the objective specifically in facilitating the substance subject to perceptible

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
A proposed model program to audit the contribution of municipal institutions to achieving the environmental dimension of sustainable development "applied research"
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Abstract

               The research aimed to prepare an audit program focusing on the activities of municipal institutions related to the environmental dimension as one of the dimensions of sustainable development, and applying the program for the purpose of preparing an oversight report related to assessing the impact of the activities of municipal institutions on the environmental reality as the main channel through which municipal institutions contribute to achieving the part related to it. Among the requirements of sustainable development, the proposed program was prepared and applied to the institutions affiliated to the Directorate of Mu

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of Engineering
Designing a Secure Software-Defined Radio Transceiver using the Logistic Map
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The need to exchange large amounts of real-time data is constantly increasing in wireless communication. While traditional radio transceivers are not cost-effective and their components should be integrated, software-defined radio (SDR) ones have opened up a new class of wireless technologies with high security.  This study aims to design an  SDR  transceiver was built using one type of modulation, which is 16 QAM, and adding a  security subsystem using one type of chaos map, which is a  logistic map, because it is a very simple nonlinear dynamical equations that generate a random key and  EXCLUSIVE  OR with the originally transmitted data to protect data through the transmission. At th

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