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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 May 01 2018
Journal Name
Journal Of Physics: Conference Series
Performance of Case-Based Reasoning Retrieval Using Classification Based on Associations versus Jcolibri and FreeCBR: A Further Validation Study
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Publication Date
Mon Sep 07 2020
Journal Name
Environmental Science And Pollution Research
The biosorption of reactive red dye onto orange peel waste: a study on the isotherm and kinetic processes and sensitivity analysis using the artificial neural network approach
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Publication Date
Wed Jul 01 2020
Journal Name
International Journal Of Pharmaceutical Research
Synthesis, Design, Docking and biological activity of new benzo hydrazide derivatives.
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Publication Date
Mon Jan 01 2018
Journal Name
Al–bahith Al–a'alami
Attitudes of University Students about the Statements of Iraqi Political Elites: A Survey Study of a Sample of University Youth in Baghdad
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Various visual media are becoming an increasingly important and active instrument of communication. This fact has led some political parties and leading personalities in Iraq to make use of them as an accepted forum for the discussion of public affairs usually in a manner that conforms to their declared policy. They have to draw as much popular support as they could for the causes which they fight for. As a result, a state of great confusion has been created from the contradictory statements made by the contending parties and gave left grave consequences on all types of the audience receiving them. The problem of the study can be summarized in one major question: What is the opinions of the audience as regards the statements made by the

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The effect of operational efficiency on some financial indicators according to the CAMEL model of banking financial stability: An applied research on a sample of Iraqi private banks for the period 2010-2020
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Abstract

          The research aims to determine the nature of the Iraqi market in terms of banking financial stability and the extent impact of the operational efficiency on it, Accordingly, chosen 15 relational banks were chosen as an intentional sample that could represent the Iraqi banking system for the period 2010-2020. The operational efficiency variable was measured according to the data envelope model, and banking financial stability used  CAMELS model which includes five indicators (capital adequacy, asset quality, management quality, profitability, and liquidity), so for testing the research hypotheses used the random regression model by adopting the S

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Publication Date
Sun Oct 01 2023
Journal Name
Journal Of Medicine And Life
Evaluating the effect of ursodeoxycholic acid (UDCA) in comparison with dexamethasone and diclofenac in a rat model of rheumatoid arthritis
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Publication Date
Sat Jul 01 2023
Journal Name
International Journal Of Research In Management
The role of network marketing for the Iraqi cement company in improving entrepreneurial behavior (An exploratory study of the opinions of a sample of company leaders)
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Publication Date
Fri Dec 29 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Synthesis and Characterization of 1, 3-Oxazepine and Benz [1, 2-e][1, 3] Oxazepine-4, 7-Diones
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N-Benzylidene m-nitrobenzeneamines (Schiff bases) were prepared by condensation of m-nitroaniline with aromatic aldehydes. These Schiff bases were found to react with maleic anhydride to give 2-Aryl-3-(m-nitrophenyl)-2, 3-dihydro [1, 3] oxazepine–4, 7–diones and with phthalic anhydride to give 2-Aryl-3–(m-nitrophenyl)–2, 3–dihydrobenz|| 1, 2-e|||| 1, 3] oxazepine–4, 7-diones which were reacted with pyrrolidine to give the anilide–pyrrolidides of maleic acid and phthalic acid.

Publication Date
Sun Jan 08 2023
Journal Name
International Journal Of Research In Social Sciences And Humanities
Evaluating Banking Performance According to the European Model of Institutional Excellence: Case Study at United Bank for Investment and Finance1
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The aim of the research is to identify the impact of the dimensions of the European Excellence Model in evaluating the performance of the bank of the research sample, as well as to interpret which dimensions are more important to the banks of the research sample. Based on the dimensions of this model, the United Bank for Investment and Finance has chosen a research community, and has met with officials of the United Bank for Investment and Finance at various administrative levels to measure the practices of excellence management in the European model, and the analytical approach has been the case study and the construction of the checklist as a tool to collect information. The research has reached the most important results There is a discr

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Publication Date
Sun Mar 02 2008
Journal Name
Baghdad Science Journal
A study of analysis and comparison to the low nutrient density foods that more normality for children age (3 –5 years)
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Through the early childhood and after the ablactating the child learns acquired food habbits that might studying with him throughout his life. Here the parents role arises: teaching the child the sound food habits and hygienic styles and whatever beneficial to the health and with the sufficient quantities for the body. In this way the experiences the child learns at home will be of great help in his future life in choosing the suitable food after becoming more dependent in making his decisions and choices away from his parents. The results in this study showed that the averages of the children’s consumption of the high energy foods in comparison with the other highest consumption average , after that comes the con sumption of soft drills

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