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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
Mon Apr 04 2022
Journal Name
Neuroquantology
The Role of Adropin as a Novel Biomarker in Iraqi Patients with Parkinson's Disease and Osteoporosis
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Publication Date
Sat Apr 02 2022
Journal Name
Neuroquantology
The Role of Neudesin as a Novel Biomarker – in Iraqi Patients with Parkinson's Disease and Osteoporosis
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Neuron-derived neurotrophic factor [NENF], a human plasma neurotrophic factor, also increases neurotrophic activity in conjunction with Parkinson's disease-related proteins in Neudesin. Although Neudesin (neuron-derived neurotrophic secreted protein) is a member of the membrane-associated progesterone receptor (MAPR) protein subclass, it is not evolutionary related to the other members of the same family. The expression of Neudesin is found in both brain and spinal cord from embryonic stages to adulthood, as w Neudesin levels in Parkinson's patients with osteoporosis disease and Parkinson's patients without osteoporosis disease, as well as the relationship between Neudesin levels, Anthropometric and Clinical Features (Age, Gender, BMI) and

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Publication Date
Wed Feb 06 2019
Journal Name
Journal Of The College Of Education For Women
The Effect use of the Internet in Academic Libraries A Case Study
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The aim of this research is to show the importance of the effective use
of the internet in academic libraries; to improve the services and to increase
the competence of librarians.
The research has given some recommendations to improve the quality
of services and the need for cooperative network among academic libraries.

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Publication Date
Fri Jul 30 2021
Journal Name
Turkish Online Journal Of Qualitative Inquiry (tojqi)
A Pragmatic Study of the Student-Teacher Relationship in the Dangerous Minds
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Publication Date
Sun Jan 01 2023
Journal Name
Journal Of Engineering
The Behavior of the Al-Kadhim Minaret during Earthquakes: A Virtual Study
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The study focuses on the causes of minaret tilting as well as possible solutions. The major aims of this study are to improve knowledge of historical tall structure stability and rehabilitation operations using the finite element approach to model the soil and minaret (PLAXIS 3D 2020), a platform for computational soil investigation and modeling. The numerical analysis aims to identify stresses, settlement, and deformation of the soil and minaret in various scenarios like Earthquakes, explosions, and winds. The simulation of the problem by the PLAXIS 3D revealed that the greatest lateral displacement computed at the Top Minaret is 5.5 cm, and the greatest vertical movement is calculated to be 3 cm. Seismic settlement is the effect of ear

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Publication Date
Wed Mar 30 2022
Journal Name
College Of Islamic Sciences
The Holy Totem in Qur’an, a study in the light of sociolinguistics
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The sacred totem is one of the social phenomena that occupied the ideas of researchers, and took up a wide area of ​​their research, and it is one of those phenomena that emerged from one of the translations of the Tabu; Who took a psychological and anthropological analysis   Because it is one of the social practices, and the main focus of it is the human group and its source is religion. Therefore, this research came with demands, the first of which is to give a semantic concept of the Tommy sanctuary, and then the analytical aspect by standing on the sacred things in the Qur’anic text that God Almighty sanctified, and the third requirement is to examine what people have sanctified, as an analysis of the verses that have

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Publication Date
Wed Nov 15 2023
Journal Name
Dirasat: Human And Social Sciences
Media Usage for Pope Francesco's Visit to Iraq March 5, 2021 (A Semiotic Study of the Photograph Welcoming Of the Pope)
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Objectives: The research aims to highlight the semiotic approach and apply it to a photograph of the Pope's reception at Baghdad International Airport, published on the page of the Media Office of Iraqi Prime Minister Mustafa Al-Kazemi in the Twitter application, in order to study its components, analyze its contents and clarify its implications, as well as approach the image as a political and media act. Methods: The stages of research were accomplished by "investigation, observation, and analysis", and the dismantling of the composition of the photograph, thus revealing the hidden and hidden aspects, relying on the semiotic approach to analysis. Results: The study showed that the ideas and meanings included in the image in form

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Publication Date
Mon Sep 30 2019
Journal Name
College Of Islamic Sciences
A book in the science of rhyme for the father of conquest Othman bin Jinni ‹v 392 e›: Investigation and study
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This book in our hands is a 'book in the science of rhymes' written by the linguistic and grammatical world 'Othman bin Jenni' 'T 392 AH', and included in it: the concept of rhyme, its characters, movements, and disadvantages, with mention of its ramifications, defining them by definition, clarification and martyrdom poetry, It is concise in size, but it is a book containing a full science in its content.
The study was divided into two parts, the first: the study, and included a study of the author and the author, I talked first about his life, such as his name and origin, and scientific status, and the words of scientists in it, and so on, and secondly: the name of the book, and his percentage, and the time of its composition, etc. I

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Publication Date
Mon May 31 2021
Journal Name
Iraqi Geological Journal
Mechanical Rock Properties Estimation for Carbonate Reservoir Using Laboratory Measurement: A Case Study from Jeribe, Khasib and Mishrif Formations in Fauqi Oil Field
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Estimation of mechanical and physical rock properties is an essential issue in applications related to reservoir geomechanics. Carbonate rocks have complex depositional environments and digenetic processes which alter the rock mechanical properties to varying degrees even at a small distance. This study has been conducted on seventeen core plug samples that have been taken from different formations of carbonate reservoirs in the Fauqi oil field (Jeribe, Khasib, and Mishrif formations). While the rock mechanical and petrophysical properties have been measured in the laboratory including the unconfined compressive strength, Young's modulus, bulk density, porosity, compressional and shear -waves, well logs have been used to do a compar

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Publication Date
Fri Nov 15 2024
Journal Name
Iraqi Journal Of Science
A Comparative Investigation of Different Ionospheric Models to Predict the MUF Parameter During Severe Geomagnetic Storm on 17th March 2015.
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The present work aimed to make a comparative investigation between three different ionospheric models: IRI-2020, ASAPS and VOACAP. The purpose of the comparative study is to investigate the compatibility of predicting the Maximum Usable Frequency parameter (MUF) over mid-latitude region during the severe geomagnetic storm on 17 March 2015. Three stations distributed in the mid-latitudes were selected for study; these are (Athens (23.50o E, 38.00o N), Jeju (124.53o E, 33.6o N) and Pt. Arguello (239.50o W, 34.80o N). The daily MUF outcomes were calculated using the tested models for the three adopted sites, for a span of five-day (the day of the event and two days preceding and following the event day). The calculated datasets were co

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