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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 01 2019
Journal Name
Environmental Earth Sciences
Urban geochemistry assessment using pollution indices: a case study of urban soil in Kirkuk, Iraq
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Publication Date
Fri Aug 02 2019
Journal Name
The Fifth Conference On Smart Monitoring, Assessment And Rehabilitation Of Civil Structures Smar 2019
Rehabilitation of Mohammed Al-Qassim Bridge after Fire Attack Using CFRP Sheets: A Case Study
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Publication Date
Wed May 17 2023
Journal Name
College Of Islamic Sciences
The origins of the structure of nominative pronouns, a linguistic study
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The Arabic pronouns received a lot of attention from the ancient Arab grammarians, so they explained their origins, the different forms of their structure, and the aspects of the Arabs’ use of them, and explained the aspects and reasons for these uses, with what they had of linguistic insight, which guided them to clarify the truth of these pronouns.
And recently, this research seeks new knowledge of the development of the structure of the nominative pronouns (he), (she), (them), (taa), and (waw) between dialects and towards classical Arabic, by analyzing the structure of these pronouns into their components. Its linguistic formulas are traced from the ancient Arabic texts, and by ancient I mean the texts of the era of linguistic ci

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Publication Date
Thu Nov 21 2024
Journal Name
Al Rafidain Journal Of Engineering Sciences
A Review of the Effect of Crumb Rubber as an Additive on Hot Mix Asphalt
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Materials recycling has a significant economic and environmental impact; as a result, steel, aluminium, plastic, and other recyclable materials have been pushed for use in construction materials. One of these recyclable materials is the crumb rubber, has been considered as a pavement component. The general behaviour of the composite rubber-hot mix asphalt system would be varied from that of the conventional rubber free mix. In this review, desirable characteristics of hot mix asphalt are highlighted first. Also, effect of gradation and the main types of rubber are specified. Afterward, many studies that considered the crumb rubber as a waste product and its associated mixture and modifiers are reviewed. The factors affect the crumb

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
Semantic (Badi'iyah)Readings in The Prophetic Praise Poetry (Mada'h Nabawiya) (Abdel Rahim Bin Ahmad Bin Ali Al Borai as a case study)
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The importance of this topic may not be overlooked by many of the specialists, because it is one the sciences of the Arabic language, but it is an important method in the field of influencing the recipient and his aesthetic ability to create influential images as well.
The talking about Semantic (Badi'iyah)is as old as the Arabic age, so it may be talking about it not the new thing because the people who specialized have preceded us and exhausted all the talk .

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Publication Date
Fri Apr 12 2019
Journal Name
Journal Of Economics And Administrative Sciences
Role of ERP In Enhancing the Accuracy of Financial Reporting
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Abstract

Nowadays, the adoption of economic unity on the accuracy of financial reporting is very important. Economic units need accurate financial reporting to be more competitive and to improve the performance. Management can also achieve financial information in real time through the application of ERP systems. This system will facilitate management to access the most up-to-date information such as planning, monitoring and evaluating the business processes of the organization to be more effective.

On the practical side, the Enterprise Resource Planning (ERP) system was applied to the General Company for Vegetable Oils to demonstrate a course in enhancing the accuracy of financial reporting.

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Publication Date
Tue Dec 31 2019
Journal Name
Biochemical & Cellular Archives
8-HYDROXY-2-DEOXY GUANOSINE IS A NOVEL NEW BIOCHEMICAL MARKER FOR PATIENTS WITH MULTIPLE SCLEROSIS AND CORRELATION WITH PARAOXANASE-1 AND MDA
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Multiple sclerosis (MS) is a chronic, inflammatory demyelinating disease of central nervous system with complex etiopathogenesis that impacts young adults (Lee et al., 2015), and MS impacts younger and middle aged character and leads to a range of disabilities that can alter their daily routines (Yara et al, 2010). Although, the exact cause of MS is still undetermined, the disease is mediated by adaptive immunity through the infiltration of T cells into the central nervous system (Bjelobaba et al, 2017). MS causes the Focal neurological symptomsand biochemical changes in the molecular level and the variation of neural cells such as loss or alteration of sensation, motor function, visible signs such as blurred vision or transient blindness,

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Publication Date
Sat Feb 02 2019
Journal Name
Journal Of The College Of Education For Women
The Balance and unbalance in alliance relations The Saudi Arabia and United State Relation as model: The Balance and unbalance in alliance relations The Saudi Arabia and United State Relation as model
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Abstract:
Saudi Arabia and United States long relation could present an important
subject to understand alliance kind in international relations types. We trying
in this study to diagnose and analyze the Saudi Arabia and United States
model to find balance and unbalance statues and its influence on the
directions of Saudi Arabia foreign policy positions.
We divided the study in two parts, each part have many sections. The
first part deal with the historian emergence of Saudi Arabia state and its
development in three stages including its foreign relations with regions and
international powers. While the second part was dedicated in analyzing and
understanding the mechanism and active facts that drawing the Sa

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Publication Date
Mon Feb 19 2018
Journal Name
Al-academy
Directing Techniques to Process the Radio Drama Script ( Khata'a Play as a Sample)
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     The radio drama is considered to be one of the arts that is discovered after a long period of theater's discovery. Initially , it was the broad framework of the theater's work when radio was broadcasting the shows on the huge theaters. This beginning encouraged many of the radio specialists to correlate plays with radio and make a novice and distinctive type of art. Thus, radio drama made its first step including the following   ( plays, short and long series drama as well as other types of radio arts). Because of the above mentioned , the researcher is stimulating  to study directing techniques to process the radio drama script ( Khata'a play as a sample).

The first chapter deals with the

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Publication Date
Sun Nov 01 2015
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Treatment of localized vitiligo with 1% pimecrolimus Cream versus 0.05% clobetasol propionate cream—single, blinded, comparative therapeutic trial
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KE Sharquie, HR Al-Hamamy, AA Noaimi, KA Ali, Journal of Cosmetics, Dermatological Sciences and Applications, 2015 - Cited by 3

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