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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
Wed Aug 13 2025
Journal Name
Al–bahith Al–a'alami
Frameworks for international press coverage of external interference in the formation of the Iraqi government Analytical study for the Saudi Al-Sharq Al-Awsat and Kayhan Al-Arabi-Iranian newspapers for the period (1/1/2018 - 31/12/2018)
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This research deals with the frameworks and mechanisms of international press coverage of the issue of foreign interference in the formation of the Iraqi government in the Saudi newspapers Asharq Al-Awsat and Kayhan Al-Arabi Iran and how this topic was addressed in the two newspapers. The frameworks for international press coverage of external interference in the formation of the Iraqi government. ”This research is one of the descriptive research that adopted the survey method، which made it possible to use the content analysis tool to analyze
the content of the two newspapers، whose numbers are (624) from the
newspapers (Al-Sharq Al-Awsat Al-Saudi Arabia and Kayhan Al-Arabi Iran) from (1/1/2018 to 31/12/2018)، and the researc

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Publication Date
Thu May 01 2025
Journal Name
Microbes And Infectious Diseases
Molecular detection and the frequency of a pore-forming toxin in Enterococcus faecalis isolated from urinary tract infections
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Publication Date
Thu Jun 15 2023
Journal Name
Journal Of Legal Sciences
Legal Protection of Computer Programs
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Computer programs are one of the most prominent features of technical progress in the field of information technology, which has raised many new issues that have not existed since the mid-twentieth century. and controls on the use of these programs by third parties, Controversy still exists about the legal nature of computer programs between those who believe that they are subject to the laws of patents and industrial property, and those who believe that they are subject to the laws of copyright protection and literary and artistic property, and the resulting difference in the scope of protection and rights established according to the legal system adopted in the application. This study comes to shed light on the legal nature of computer

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Publication Date
Sat May 30 2020
Journal Name
Neuroquantology
Comparative Study for Optoelectronic Properties of Zn (Te, Se) Solar Cells
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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Comparative Study of Gamma- Ray Shielding Parameters for Different Epoxy Composites
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In the current work various types of epoxy composites were added to concrete to enhance its effectiveness as a gamma- ray shield. Four epoxy samples of (E/clay/B4C) S1, (E/Mag/B4C) S2, (EPIL) S3 and (Ep) S4 were used in a comparative study of gamma radiation attenuation properties of these shields that calculating using Mont Carlo code (MCNP-5). Adopting Win X-com software and Artificial Neural Network (ANN), µ/ρ revealed great compliance with MCNP-5. By applying (µ/ρ) output for gamma at different energies, HVL, TVL and MFP have been also estimated. ANN technique was simulated to estimate (µ/ρ) and dose rates. According to the results, µ/ρ of all epoxy samples scored higher than standard concrete. Both S2 and S3 samples having h

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Publication Date
Wed Oct 09 2019
Journal Name
Journal Of The College Of Education For Women
Silence as a Means of Communication in Harold Pinter’s The Caretaker
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Harold Pinter’s The Caretaker(1959) clearly portrays a lack of communication among the characters of the play which refers to the condition of modern man. This failure of communication led Harold Pinter to use a lot of pauses and silences in all the plays he wrote instead of words. Samuel Beckett preceded Pinter in doing so in his plays and one way to express the bewilderment of modern man during the 20th century is through the use of no language in the dramatic works. Language is no more important to modern man; instead, he uses silence to express his feelings. Silence is more powerful than the words themselves. That’s why long and short pauses can be seen throughout all Pinter’s plays.

In this play, th

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Publication Date
Sun Dec 31 2006
Journal Name
Journal Of Engineering
Theoretical Simulation Of Stress-Strain Relations For Some Iraqiclays Using The Endochronic Model
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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Handling a problem of transport solid waste in Baghdad City to Healthy landfill sites using transportation Model
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 A problem of solid waste became in the present day common global problem among all countries, whether developing or developed countries, and can say that no country in the world today is immuning from this dilemma which must find appropriate solutions. The problem has reached a stage that can not ignore or delay, but has became a daily problem occupies the minds of ecologists, economists and politicians took occupies center front in the lists of  priorities for the countries in terms of finding solutions to the rapid scientific and radical them. and that transport costs constitute an important component of total costs borne by the municipal districts in the process of disposal of solid waste, so any improvement in the

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Probabilistic Model building using the Transformation Entropy for the Burr type –xii Distribution
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Entropy define as uncertainty measure has been transfared by using the cumulative distribution function and reliability function for the Burr type – xii. In the case of data which suffer from volatility to build a model the probability distribution on every failure of a sample after achieving limitations function, probabilistic distribution. Has been derived formula probability distribution of the new transfer application entropy on the probability distribution of continuous Burr Type-XII and tested a new function and found that it achieved the conditions function probability, been derived mean and function probabilistic aggregate in order to be approved in the generation of data for the purpose of implementation of simulation

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative Assessment of in Vitro Effect of Three Fluoride Releasing Agents on Enamel Demineralization around Orthodontic Brackets
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