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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 Mar 30 2013
Journal Name
College Of Islamic Sciences
The comparative approach (stabilizer) and the need for Arabic to it
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Linguistic research according to modern curricula:
   It is one of the important matters that occupy the ideas of those concerned with linguistic studies, whether Arabic or otherwise. Recent years have witnessed the advancement of this methodological approach, and books and studies in Arabic have been written on important, multifaceted issues, of grammatical and linguistic origins, and their balance with new developments and ideas attracted mostly from Western studies.
    The comparative approach - as they call it - is one of the modern approaches that is based on balancing a language with other sisters belonging to its family, to reach similarities and differences between them, and to know the c

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Prepare a plan for the Total Productive Maintenance in the light of the concurrent engineering A Field Study in AL-Askandria General Company Machanical Industries and AL-Musaib Electric Power Station
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           Strives Total Productive Maintenance  to increase the overall effectiveness of the equipment through the early involvement in the design and manufacture of equipment productivity. It also operates in an environment of simultaneous engineering work on the synchronization of activities to take advantage of early information by maintenance engineers, design, operation, and that helps to reduce the faults and facilitate future maintenance tasks.

    Has adopted a search in the theoretical concept of the total maintenance productivity and concurrent engineering activities carried out during which the conjunction a

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Publication Date
Tue Jun 01 2021
Journal Name
International Journal Of Nonlinear Analysis And Applications
A proposed method for cleaning data from outlier values using the robust rfch method in structural equation modeling
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Publication Date
Fri Nov 15 2024
Journal Name
Iraqi Journal Of Science
A Comparative Investigation of Different Ionospheric Models to Predict the MUF Parameter During Severe Geomagnetic Storm on 17th March 2015.
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The present work aimed to make a comparative investigation between three different ionospheric models: IRI-2020, ASAPS and VOACAP. The purpose of the comparative study is to investigate the compatibility of predicting the Maximum Usable Frequency parameter (MUF) over mid-latitude region during the severe geomagnetic storm on 17 March 2015. Three stations distributed in the mid-latitudes were selected for study; these are (Athens (23.50o E, 38.00o N), Jeju (124.53o E, 33.6o N) and Pt. Arguello (239.50o W, 34.80o N). The daily MUF outcomes were calculated using the tested models for the three adopted sites, for a span of five-day (the day of the event and two days preceding and following the event day). The calculated datasets were co

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Publication Date
Tue Nov 01 2022
Journal Name
Optik
Design new D-π-A materials for sensitizers for dye-sensitized solar cells: Quantum chemical study
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Within this paper, we developed a new series of organic chromophores based on triphenyleamine (TPA) (AL1, AL-2, AL-11 and AL-22) by engineering the structure of the electron donor (D) unit via replacing a phenyle ring or inserting thiophene as a π-linkage. For the sake of scrutinizing the impact of the TPA donating ability and the spacer upon the photovoltaic, absorptional, energetic, and geometrical characteristic of these sensitizers, density functional theory (DFT) and time-dependent DFT (TD-DFT) have been utilized. According to structural characteristics, incorporating the acceptor, π-bridge and TPA does not result in a perfect coplanar conformation in AL-22. We computed EHOMO, ELUMO and bandgap (Eg) energies by performing frequency a

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Publication Date
Sat Nov 27 2021
Journal Name
Route Educational & Social Science Journal
A STYLISTIC ANALYSIS OF ADVERTISING DISCOURSE: A CASE STUDY OF FACEBOOK COMMERCIAL ADVERTISEMENT
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BN Rashid

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of The College Of Languages
The Outcomes of War: A Study of the Character After the Crisis of War
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World War II has brought suffering for all people; it has led people to have a nostalgic feeling. The war has many faces all of them are ugly, like death, separation, loneliness, violence, crime, betrayal, and disconnection and many other meanings. Michael Ondaatje in his novel The English Patient (1992) portrays a picture of the effect of World War II on four different characters; Hana a Canadian nurse, The English patient who is Hungarian, Caravaggio a Canadian-Italitan thief, and Kip an Indian sapper. They live together in one house, share their secrets and memories about World War II. Ondaatje brings them together to reveal their secrets and to heal their wounds of the war experience.

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of The College Of Languages (jcl)
The Outcomes of War: A Study of the Character After the Crisis of War
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World War II has brought suffering for all people; it has led people to have a nostalgic feeling. The war has many faces all of them are ugly, like death, separation, loneliness, violence, crime, betrayal, and disconnection and many other meanings. Michael Ondaatje in his novel The English Patient (1992) portrays a picture of the effect of World War II on four different characters; Hana a Canadian nurse, The English patient who is Hungarian, Caravaggio a Canadian-Italitan thief, and Kip an Indian sapper. They live together in one house, share their secrets and memories about World War II. Ondaatje brings them together to reveal their secrets and to heal their wounds of the war experience.

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Publication Date
Sun Jul 17 2022
Journal Name
Al–bahith Al–a'alami
(دراسة تحليلية): ( A field study )
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The research aimed to identify the effects of the modern of technology on translating the media term from English language to Arabic. and try to identify the use of the impact of foreign media terminologies on the Arabic media term, and to know the effect of the translation process on Arabic media terminologies.

This research is considered an analytical study by using survey study for 111 items and the results for the study as following:

1.High percentage of the (use of foreign terms work to low the level of production) was (68.13%) and average 3.55

2.The percentage of (The multiplicity of translation of the foreign term into Arabic effects on the opinions and cognitive ideas of the Arab researcher and affects the

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Publication Date
Tue Feb 09 2016
Journal Name
Advances In Environmental Biology
A study effect Histological changes
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