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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
Sat Jan 01 2022
Journal Name
Journal Of The Mechanical Behavior Of Materials
Time and finance optimization model for multiple construction projects using genetic algorithm
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Abstract<p>Construction contractors usually undertake multiple construction projects simultaneously. Such a situation involves sharing different types of resources, including monetary, equipment, and manpower, which may become a major challenge in many cases. In this study, the financial aspects of working on multiple projects at a time are addressed and investigated. The study considers dealing with financial shortages by proposing a multi-project scheduling optimization model for profit maximization, while minimizing the total project duration. Optimization genetic algorithm and finance-based scheduling are used to produce feasible schedules that balance the finance of activities at any time w</p> ... Show More
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Publication Date
Sun Dec 18 2022
Journal Name
Journal Of The College Of Basic Education
A (k,ℓ) Span in Three Dimensional Projective Space PG(3,p) Over Galois Field where p=4
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الغرض من هذا العمل هو دراسة الفضاء الإسقاطي ثلاثي الأبعاد PG (3، P) حيث p = 4 باستخدام المعادلات الجبرية وجدنا النقاط والخطوط والمستويات وفي هذا الفضاء نبني (k، ℓ) -span وهي مجموعة من خطوط k لا يتقاطع اثنان منها. نثبت أن الحد الأقصى للكمال (k، ℓ) -span في PG (3،4) هو (17، ℓ) -span ، وهو ما يساوي جميع نقاط المساحة التي تسمى السبريد.

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of The College Of Languages (jcl)
Metaphor in Political Discourse Press Articles By Louis Bassets As A Model: La metáfora en el discurso político. Los artículos de Lluís Bassets como ejemplo
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       The present paper focuses on studying a rhetorical form often used in Spanish linguistic discourse .It also examines the study two sides (theoretical and practical), the concept of metaphor, the most important modern school that deals with this issue, the development of this technique and its relationship with other intellectual ideologies, and the role metaphor plays in interpreting the meaning of the linguistic discourse especially in conveying political message. The study allows the formulation and the creation of a conceptual picture for the purposes of metaphor in the linguistic discourse used in Spanish press. It investigates discursive models from the Spanish press,

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Publication Date
Wed Jan 26 2022
Journal Name
Iraqi Journal Of Science
Potentiometric Determination of Mebeverine Hydrochloride Using Imprinted Molecular Polymer in PVC Matrix Membrane‏
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Publication Date
Fri Dec 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Comparing the effectiveness of using three different re-mineralizing pastes on remineralisation of artificially induced white spot lesion
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Background: This study aimed to compare the surface microhardness (MH) and mineral content of white spot lesions(WSLs) after using bioactive glass (BAG)casein phosphopep-tides-amorphous calcium phosphate(CPP-ACP),and nanohydroxyapatite(Nano-HAP) under pHcycling. Material and method:18 sound maxillary first premolar were used for the study.10 were selected for the vickers microhardness test, For Energy-dispersive X-ray spectroscopy analysis (EDX), the remaining 8 premolar teeth were used, 40 sections of enamel blocks (Four from each tooth) were produced from the middle part of the buccal and palatal surfaces of teeth for MH test while 48 sections of enamel blocks (Six from each tooth) were produced for EDX analysis. Enamel slabs were

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Publication Date
Fri Dec 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Comparing the effectiveness of using three different re-mineralizing pastes on remineralisation of artificially induced white spot lesion
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Background: This study aimed to compare the surface microhardness (MH) and mineral content of white spot lesions(WSLs) after using bioactive glass (BAG)casein phosphopep-tides-amorphous calcium phosphate(CPP-ACP),and nanohydroxyapatite(Nano-HAP) under pHcycling. Material and method:18 sound maxillary first premolar were used for the study.10 were selected for the vickers microhardness test, For Energy-dispersive X-ray spectroscopy analysis (EDX), the remaining 8 premolar teeth were used, 40 sections of enamel blocks (Four from each tooth) were produced from the middle part of the buccal and palatal surfaces of teeth for MH test while 48 sections of enamel blocks (Six from each tooth) were produced for EDX analysis. Enamel slabs were divi

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Publication Date
Tue Dec 20 2022
Journal Name
Biomedical And Pharmacology Journal
Phytochemical Comparison Study for Evaluating the Hypolipidemic Effect Between Two Iraqi Pepper Spp in the Rats Model.
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Hypercholesterolemia is a predominant risk factor for atherosclerosis and cardiovascular disease (CVD). The World Health Organization (WHO), ) recommended reducing the intake of cholesterol and saturated fats. On the other hand, limited evidence is available on the benefits of vegetables in the diet to reduce these risk factors, so this research was conducted to compare the hypolipidemic effect between the extracts of two different types of Iraqi peppers, the fruit of the genus Capsicum traditionally known as red pepper extract (RPE), and Piper nigrum as black pepper extract (BPE), respectively, in different parameters and histology of the liver of the experimental animals. The red pepper was extracted by ethyl acetate, while the black pepp

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Publication Date
Wed Jun 29 2022
Journal Name
Journal Of The College Of Education For Women
The Chicago School in Urban Sociology: A Socio-Historical Approach on the Pragmatic Thought Influence as a Theoretical Frame of Reference in it-1892-2020
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The present theoretical study analyzes the legacy of the Chicago School of Urban Sociology and evaluates it in the light of the growth and development of Chicago City and the establishment of sociology in it. Sociology has become an academic discipline recognized in the United States of America in the late nineteenth century, particularly, after the establishment of the first department of sociology in the University of Chicago in 1892. That was during the period of the rapid industrialization and sustainable growth of the Chicago City. The Chicago School relied on Chicago City in particular, as one of the American cities that grew and expanded rapidly in the first two decades of the twentieth century. At the end of the nineteenth centur

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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
Political finance: a study on the financing of political parties
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 Parties as active units in this process in order to work must have access to sources of funding in order to maintain their political presence in society and participate in the process of electoral competition, To win the election, bolstering the huge role that money has played in influencing the principle of equality among contestants in the elections. Those who own money will have a greater chance of winning the elections while less competitive opportunities for others who do not own the money or what they own does not give them the competitive ability to win elections. From this point of view, controlling political finance through legal regulation and institutional, media and popular monitoring has become an important requirement

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Publication Date
Thu Sep 30 2021
Journal Name
International Journal Of Research In Social Sciences And Humanities
The Anonymous Identity of Forced Migrants: A Post-Colonial Study
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Colonialism invades the Third World countries, physically and psychologically. This article exposes but sample of the physical and psychological consequences of colonialism. The Beekeeper of Aleppo (2019) by the British novelist, Christy Lefteri is a typical novel to diagnose the harsh circumstances of individuals within and after the disaster. Since it depicts characters from Asian countries, it would be a best representative for all Asian people who suffer colonialism. Migration toward anonymity is the mere option for the colonized people. Aftermath, they experience displacement, trauma, and the loss of identity.

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