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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 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
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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Publication Date
Tue Jun 20 2023
Journal Name
Bulletin Of The Iraq Natural History Museum
A COMPARATIVE-MORPHOLOGICAL STUDY OF SKULLS IN TWO SPECIES OF CARNIVOROUS AND HERBIVOROUS MAMMALS
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The skull is one of the largest bones in the body. It is classified into flat bones that maintain the important organic structures; which are the brain, eyes, and tongue. The skull is a strong support for preserving these organs but they are various according to the type of animals and the environments in which they live and the nature of their nutrition. There are many differences among living organisms in terms of the bones in the skull, their difference or disappearance and their length in the shape of the head. The samples were taken from the scientific storage in the Iraq Natural History Research Center and Museum; Cape hare Lepus capensis (Linnaeus, 1758) and Red fox Vulpes vulpes (Linnaeus, 1758) and the study was conducted o

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Publication Date
Sun Feb 18 2024
Journal Name
Fitness, Performance And Health Journal
A Comparative Study of Some Types of Muscular Strength Among Middle-Distance Runner Athletes
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The research aims to conduct a comparative study between the events (800) m and (1500) m track in the types of muscular strength and to identify the differences between them among Iraqi sports club players. The sample represented the players participating in the Iraqi Athletics Championship for the period between (02/11/2023) and (04 /11/2023), and their number was (16) players (8) for each event, as the selection was made intentionally.  The researchers used the descriptive approach to achieve the goal of the research and used the statistical package (SPSS) to process the data statistically. According to the results collected, it was found that there was superiority among the intermediate track players (800) m in explosive power and the s

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Publication Date
Tue Jun 20 2023
Journal Name
Bulletin Of The Iraq Natural History Museum
A COMPARATIVE-MORPHOLOGICAL STUDY OF SKULLS IN TWO SPECIES OF CARNIVOROUS AND HERBIVOROUS MAMMALS
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The skull is one of the largest bones in the body. It is classified into flat bones that maintain the important organic structures; which are the brain, eyes, and tongue. The skull is a strong support for preserving these organs but they are various according to the type of animals and the environments in which they live and the nature of their nutrition. There are many differences among living organisms in terms of the bones in the skull, their difference or disappearance and their length in the shape of the head. The samples were taken from the scientific storage in the Iraq Natural History Research Center and Museum; Cape hare Lepus capensis (Linnaeus, 1758) and Red fox Vulpes vulpes (Linnaeus, 1758) and the study was conducted o

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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
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Spectroscopic Study for Determination of Amoxicillin Using Cobalt(II) as Complexing Metal
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         This study includes analytical methods for the determination of the drug amoxicillin trihydrate (Amox.) in some pharmaceutical preparations using Cobalt ion (Co(II)) as complexing metal. The best conditions for complexation were: the reaction time was 20 minutes, pH=1.5 and the best temperature of reaction was 70 ËšC. Benzyl alcohol was the best solvent for extraction the complex.

Keywords: Amoxicillin, Cobalt(II), Complex, Molar ratio.

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Publication Date
Wed Oct 28 2015
Journal Name
Journal Of Mathematics And System Science
Simulating Particle Swarm Optimization Algorithm to Estimate Likelihood Function of ARMA(1, 1) Model
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Publication Date
Thu Nov 13 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Immunohistochemical expression of MMP1 and TIMP1 as markers of migration in Hodgkin’s and non-Hodgkin’s lymphoma of the head and neck region (A comparative study)
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Background: Malignant lymphoma is a term that describes primary tumors of the lymphoreticular system, almost all of which arise from lymphocytes.MMP-1 is the most ubiquitously expressed interstitial collagenase, a subfamily of MMPs that cleaves stromal collagens. It is also called collagenase-1.TIMPs which inhibits MMP activity and thereby restrict extracellular matrix breakdown, TIMP-1 is a stromal factor that has a wide spectrum of functions in different tissues. Material and Methods: This study was performed on (68) formalin-fixed, paraffin-embedded blocks, histopathologically diagnosed as lymphoma (head and neck lesions). Immunohistochemical staining of MMP1and TIMP1 was performed on each case of the study sample. Results: The expressio

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