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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
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
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 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
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
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 Oct 20 2022
Journal Name
Iraqi Journal Of Industrial Research
Study of the Effect of Epipremnum Aureum Extracts and Tribulus Terrestris L. as a Natural Alternative for the use of Industrial Antioxidants
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In this study, two types of local plants were chosen, the first is the plant golden pothos Epipremnum aureum and the second is the Iraqi Sheikh's chin plant Tribulus terrestris L, for the purpose of making a comparison between them in terms of their possession of chemical groups with antioxidant activity in order to use them as a natural alternative to using antioxidants Industrial that cause negative effects on human health, the samples were prepared using the method of water and alcohol extraction (ethanol 70%) for both plants. It revealed the presence of a number of chemical groups (tannins, carbohydrates, phenols, flavonoids, alkaloids) for both plants, the aqueous and alcoholic extracts. Coumarins are only found in the sheikh's chin pl

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Publication Date
Tue Oct 11 2022
Journal Name
College Of Islamic Sciences
The Jurisprudence rule and its impact on Islamic legislation “Forcing does not nullify the rights of others” as a model .
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Research Summary :

         Praise be to God, Lord of the Worlds, and prayers and peace be upon the Master of the Messengers, his family and all his companions, then after:

     This is brief research that contained between its two covers one of the jurisprudence rules derived from Islamic Sharia that guarantees the right of others, in case of forcing to do the prohibited act, and it is a restriction of the rule: “Necessities allow prohibitions” and “Hardship brings facilitation” and support for the rule: “Necessities are valued.” It is an origin in alleviating the taxpayer definitely , and the study has briefly shown some of the jurisprudential appli

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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
Wed Nov 30 2022
Journal Name
Iraqi Geological Journal
A Predictive Model for Estimating Unconfined Compressive Strength from Petrophysical Properties in the Buzurgan Oilfield, Khasib Formation, Using Log Data
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Unconfined compressive strength (UCS) of rock is the most critical geomechanical property widely used as input parameters for designing fractures, analyzing wellbore stability, drilling programming and carrying out various petroleum engineering projects. The USC regulates rock deformation by measuring its strength and load-bearing capacity. The determination of UCS in the laboratory is a time-consuming and costly process. The current study aims to develop empirical equations to predict UCS using regression analysis by JMP software for the Khasib Formation in the Buzurgan oil fields, in southeastern Iraq using well-log data. The proposed equation accuracy was tested using the coefficient of determination (R²), the average absolute

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Publication Date
Tue Jun 15 2021
Journal Name
Al-academy
The concept of freedom in the texts of Yashar Kamal play "The play (The Plate) as a model": عامر صباح نوري المرزوك
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This research is concerned with studying (the concept of freedom in the texts of Yaşar Kamal the play), as the Turkish playwright (Kamal Yasar) is one of the contemporary playwrights who have been interested in and criticize society, and perhaps the concept of freedom in his texts took a different form, through his ability to renew and present his attempts to create A theatrical form different from his earlier writers in dealing with the life of the peasants and the oppression that went through them, as the researcher identified the problem of his research with the following question: What is the concept of freedom in the texts of Yashar Kamal? The research aims to define the concept of freedom in the texts of Yashar Kamal of the play,

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