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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
Thu Nov 01 2012
Journal Name
Journal Of The Faculty Of Medicine Baghdad
A Comparative Study of the Effects of Age and Smoking on Nail Growth Rate in Healthy Individuals
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GA Al Omran, AA Noaimi, Z Al Madfai, H Al Hamamy, Journal of the Faculty of Medicine Baghdad, 2012

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Publication Date
Thu May 30 2024
Journal Name
Proximus Journal Of Sports Science And Physical Education
A COMPARATIVE STUDY OF THE MOST IMPORTANT PERSONALITY TRAITS BETWEEN PRACTITIONERS AND NON-PRACTITIONERS OF SPORTS ACTIVITY
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The researchers reached many conclusions, the most important of which was the distinction of practitioners of sports activity with high degrees in the trait (social). At the same time, it was low in the trait (aggression –restraint-desisting) and non-practitioners were distinguished by sports activity with high degrees in the trait (aggression –restraint-desisting). In contrast, the degree was low in the trait (social), and there were significant differences in favor of practitioners of the activity of the athlete, Through the conclusions, the researchers recommend the need for university students to practice sports activities because of their positive impact on their health in general and on the deve

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
A comparative study of the effects of argon laser and continuous Nd: YAG laser on blood vessel
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Several types of laser are used in experimental works in order to study the effects of laser on blood vessel. They differ from each other by a lot of properties mainly in wavelength, energy of the laser and pulse duration. In this study argon laser (488 nm- 514 nm) and continuous Nd: YAG laSer (1064 nm), have been applied to 50 samples of sheep blgod tesselS. Histologically, tha results of the study were different According to the txpe of L`sar used; apgon larer had distrabtave effects on $he blood vessal while continuous Nd: YAG laser Appeaped to be the safesd one on the blmod vessel architecture. This study concluded that argoj laser has da-aging ef&ect on

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Publication Date
Tue Apr 01 2025
Journal Name
Iop Conference Series: Earth And Environmental Science
A Comparative Study of Organic and Mineral Acids in the Release of Potassium from Potassium Feldspar Minerals
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Abstract<p>A study conducted a laboratory experiment to measure the release of potassium and the dissolution of feldspar minerals in soils from different locations in Karbala Province (Ain Al-tamur, Qasr Al-Akhyar, Fadak Farm). The study involved the addition of organic acids (fulvic and humic) and mineral acids (sulfuric and phosphoric) at concentrations of 5% and 10% to sand-separated soil samples obtained through wet sieving. Feldspar minerals were identified using a polarized light microscope, and the percentage of each type of feldspar mineral was calculated. The results demonstrated that organic acids outperformed mineral acids in releasing potassium at both concentrations. Among the organ</p> ... Show More
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Publication Date
Sun May 02 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Value at risk simulation in a fixed return stock portfolio using the Monte Carlo simulation model The concept of a bond portfolio
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This research aims to predict the value of the maximum daily loss that the fixed-return securities portfolio may suffer in Qatar National Bank - Syria, and for this purpose data were collected for risk factors that affect the value of the portfolio represented by the time structure of interest rates in the United States of America over the extended period Between 2017 and 2018, in addition to data related to the composition of the bonds portfolio of Qatar National Bank of Syria in 2017, And then employing Monte Carlo simulation models to predict the maximum loss that may be exposed to this portfolio in the future. The results of the Monte Carlo simulation showed the possibility of decreasing the value at risk in the future due to the dec

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Publication Date
Mon Nov 28 2016
Journal Name
Separation Science And Technology
Using sewage sludge as a permeable reactive barrier for remediation of groundwater contaminated with lead and phenol
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Publication Date
Tue Jun 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Evaluating the effects of reservoir level and foundation depth on the dynamic behaviour of a rockfill dam using three-dimensional finite elements modelling
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Abstract<p>This paper presents a three-dimensional Dynamic analysis of a rockfill dam with different foundation depths by considering the dam connection with both the reservoir bed and water. ANSYS was used to develop the three-dimensional Finite Element (FE) model of the rockfill dam. The essential objective of this study is the discussion of the effects of different foundation depths on the Dynamic behaviour of an embanked dam. Four foundation depths were investigated. They are the dam without foundation (fixed base), and three different depths of the foundation. Taking into consideration the changing of upstream water level, the empty, minimum, and maximum water levels, the results of the three-dimensional F</p> ... Show More
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Publication Date
Tue Jul 01 2014
Journal Name
International Journal Of Artificial Intelligence And Mechatronics
Building a Three-Axis CNC Milling Machine Control System
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CNC machines are widely used in production fields since they produce similar parts in a minimum time, at higher speed and with possibly minimum error. A control system is designed, implemented and tested to control the operation of a laboratory CNC milling machine having three axes that are moved by using a stepper motor attached to each axis. The control system includes two parts, hardware part and software part, the hardware part used a PC (works as controller) connected to the CNC machine through its parallel port by using designed interface circuit. The software part includes the algorithms needed to control the CNC. The sample needs to be machined is drawn by using one of the drawing software like AUTOCAD or 3D MAX and is saved in a we

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Publication Date
Mon Feb 19 2018
Journal Name
Al-academy
The Mechanisms of build up the dramatic construction in the films of the world of nature - National Geographic's films as a model-
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The subject of  research entitled "The Mechanisms of build up the dramatic construction in the films of the world of nature - National Geographic's films as a model" emerges from the importance of the subject of the dramatic construction and its departure from its classic style due to the evolution of the visual  presentation and its instruments and the specificity and emergence of a form of television production represented by the films of the world of nature which began to occupy an important space in the map of television and television channels specialized in this subject, which drove the researcher to study the mechanisms of producing the dramatic construction in this kind of film s. This research came in three  chapt

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Publication Date
Thu Nov 02 2023
Journal Name
Journal Of Engineering
Constructing a Sustainable Roller Compacted Concrete Using Waste Demolished Material as Replacement of Cement: A Review
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Roller Compacted Concrete is a type of concrete that is environmentally friendly and more economical than traditional concrete. Roller Compacted Concrete is typically used for heavy-duty and specialist constructions, such as hydraulic structures and pavements, because of its coarse surface. The main difference between RCC and conventional concrete mixtures is that RCC has a more significant proportion of fine aggregates that allow compaction and tight packing. In recent years, it has been estimated that several million tons of waste demolished material (WDM) produced each year are directed to landfills worldwide without being recycled for disposal. This review aimed to study the literature about creating a Roller-Comp

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