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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 Dec 30 2025
Journal Name
Alnahrain Journal Of Legal Scienci
Elements and Conditions of Personal Civil Liability (Based on Fault) for the Government for Damages Caused by Demonstrations: A Comparative Study
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This study examines the position of comparative legislation (French legislation, English legislation, and Egyptian legislation) in addressing the regulation of personal civil liability (based on fault) for the government. About the damages caused by demonstrations in terms of their legal nature, their legal basis, and the pillars and conditions of that responsibility. Then, we explain the position of the Iraqi legislator and compare it with what is the case in the legislation mentioned above

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Publication Date
Mon Sep 12 2016
Journal Name
Revista Pesquisa Em Fisioterapia
YOGA AS A TREATMENT FOR MUSCULOSKELETAL DISCOMFORTS: A HYPOTHESIS
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Introduction: Nowadays, the prevalence of Musculoskeletal Discomforts (MSD) is increasing in the world. As treatment, usually surgery or physiotherapyare recommended, but they are expensive and may cause side effects. Apracticalcourse of treatment without negative side effects and with permanent positive effects is lacking. Objective: To suggest a practical course of treatment, introduced by a licensed Yoga coach who is experienced in this field, and through thatto shed a light on yoga as treatment for MSD. The hypothesis is that yoga may decrease the pain among individuals with MSD. Methods: This hypothesis is presented based on the practical techniques used in Yoga including body relaxation and breathing awareness (2 minutes & 3 minutes r

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
ETHICAL JOURNALISM IN IRAQ AFTER 2003: Baghdad edition as a model
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The fact of having Journalism being open to people from different orientations professions, working as journalists requiring protection just to spread corruption, is one of the biggest threats faced by journalism.

Journalists noticed the spread of unprincipled journalists with no journalistic ethics amongst them, they tried to protect their profession from these corrupt outsiders who might annihilate the mighty of journalism. The principles of the journalism profession known as journalistic ethics, are one the most important formulations of the law concluded by the journalists and those concerned by the the profession, they were then published in public in order to prove their professionalism, especially for those who don’t und

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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Legal Sciences
Judicial Tools in Developing Civil Law Rules – France as a Model
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Despite the principle of separation of powers brought by the French Revolution, which entrusted the task of drafting legislation and its amendment to the legislative authority and the task of settling disputes and settling them in the judiciary. However, since that date, the French judiciary has played a major role in the development of French civil law (In spite of all the economic and social developments that have taken place in French society throughout these years) since its promulgation until February of 2016, the date of the Legislative Decree No. 131 of the year 2016 A modification is the largest in the history of the French Civil Code (which was the judicial precedents in which a significant impact), was assisted by the French judic

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Publication Date
Fri Dec 15 2023
Journal Name
Al-academy
Design contexts in interior space design (sewing workshops as a model)
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The topic of context is one of the important topics, which was mentioned as a concept in several fields and different fields, and there were many points of view that defined that concept.
He specified the title of the research (design contexts in the design of the interior space), as the research sought to identify the concept of context in the interior design of the spaces of sewing workshops. The research was divided into four chapters:
The first chapter, which consists of the methodological framework, the problem of research and the need for it, the importance of research, the goal and limits of research for sewing workshops for vocational schools from (2020-2021).
The second chapter: consists of previous studies and the theo

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Publication Date
Wed Sep 15 2021
Journal Name
Al-academy
Processes directing the scenography space in the Iraqi theatrical show Shakespeare texts as a model
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Publication Date
Wed Sep 15 2021
Journal Name
Al-academy
Processes directing the scenographic space in the Iraqi theatrical show Shakespeare texts as a model
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Publication Date
Tue Dec 25 2018
Journal Name
Summaries Of Working Papers, Research And Experiments
E-learning at the College of Mass Communication, subject: public relations campaigns as a model
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Publication Date
Sat Jun 01 2024
Journal Name
Pakistan Journal Of Criminology
Artificial Intelligence Technology in the Field of Modern Forensic Evidence: Brain Fingerprinting as a Model
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Brain Fingerprinting (BF) is one of the modern technologies that rely on artificial intelligence in the field of criminal evidence law. Brain information can be obtained accurately and reliably in criminal procedures without resorting to complex and multiple procedures or questions. It is not embarrassing for a person or even violates his human dignity, as well as gives immediate and accurate results. BF is considered one of the advanced techniques related to neuroscientific evidence that relies heavily on artificial intelligence, through which it is possible to recognize whether the suspect or criminal has information about the crime or not. This is done through Magnetic Resonance Imaging (EEG) of the brain and examining

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Publication Date
Thu Sep 01 2022
Journal Name
Natural Product Research
Synthesis, molecular docking and anti-inflammatory evaluation of new trisubstituted pyrazoline derivatives bearing benzenesulfonamide moiety
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