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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
Thu Nov 18 2021
Journal Name
Iraqi Journal Of Physics
The study of nuclear structure for some nuclei
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An analytical form of the ground state charge density distributions
for the low mass fp shell nuclei ( 40  A  56 ) is derived from a
simple method based on the use of the single particle wave functions
of the harmonic oscillator potential and the occupation numbers of
the states, which are determined from the comparison between theory
and experiment.
For investigating the inelastic longitudinal electron scattering form
factors, an expression for the transition charge density is studied
where the deformation in nuclear collective modes is taken into
consideration besides the shell model space transition density. The
core polarization transition density is evaluated by adopting the
shape of Tassie mod

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Publication Date
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Physics
The study of nuclear structure for some nuclei
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 An analytical form of the ground state charge density distributions
for the low mass fp shell nuclei ( 40  A  56 ) is derived from a
simple method based on the use of the single particle wave functions
of the harmonic oscillator potential and the occupation numbers of
the states, which are determined from the comparison between theory
and experiment.
For investigating the inelastic longitudinal electron scattering form
factors, an expression for the transition charge density is studied
where the deformation in nuclear collective modes is taken into
consideration besides the shell model space transition density. The
core polarization transition density is evaluated by adopting the
shape of Tass

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Publication Date
Mon May 11 2020
Journal Name
Journal Of Arts, Literature, Humanities And Social Sciences
The Kite Runner; A Journey of Growth
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Publication Date
Thu Jan 01 2015
Journal Name
Algebra Letters
THE GRAPH OF A COMMUTATIVE KU-ALGEBRA
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In This paper, we introduce the associated graphs of commutative KU-algebra. Firstly, we define the KU-graph which is determined by all the elements of commutative KU-algebra as vertices. Secondly, the graph of equivalence classes of commutative KU-algebra is studied and several examples are presented. Also, by using the definition of graph folding, we prove that the graph of equivalence classes and the graph folding of commutative KU-algebra are the same, where the graph is complete bipartite graph.

Publication Date
Tue Oct 01 2024
Journal Name
Computational And Theoretical Chemistry
The curious case of S4N4 − A reinvestigation
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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Towards building an educational system free of scientific corruption (Applied study in a sample of colleges of higher education in Iraq within the framework of the government program and the directions of the Supreme Council for Combating Corruption)
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Nations are developed with education and knowledge that raise the status of society in its various segments, beyond that it leads to underdevelopment and deterioration in various sectors, whether economic, health, social, etc. If we considered the general name of The ministry of Education & Scientific Studies, then the second part seems to be not functioning, since scientific research has no material allocation and remains based on the material potential of the university professor. As for the first half of the topic, the reality of the situation reveals problems related to the Holy Trinity of Education which is (Professor - Student - the scientific method) where universities suffer at the present time from this problem, and

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Publication Date
Mon Dec 03 2018
Journal Name
The Iraqi Postgraduate Medical Journal
Operative Treatment by Plate and Screws Versus Conservative Treatment of Closed Displaced Fracture of the Mid Third of Clavicle in Adults: Comparative Study
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BACKGROUND: Clavicle fractures are common injuries in young active individuals, the mid third of the clavicle is most commonly fractured part(80% of clavicle fracture) OBJECTIVE: To compare the outcomes of operative and non operative management of displaced and or comminuted closed fracture of the mid third of clavicle in young adults PATIENTS AND METHODS: This prospective observational study of 24 patients of fracture of the mid third of the clavicle was conducted in Alkindy teaching hospital from July 2015 to January 2017 and divided into two groups; one managed by operative treatment with plate and screws and the other by non operative sling immobilization after taking the consent and the patients were seen at 2, 4, 6 weeks,3, 6, and 9 m

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Publication Date
Thu Jun 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
The Workplace Fun as Moderator Variable between Leadership Virtuousness and Organizational Brilliance (Applied study at the University of Kufa)
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Abstract

    The current research tested the interactive role between the workplace fun and the leadership virtuousness in the organizational brilliance, in a sample of the teaching staff at the University of Kufa reached (325 staff) out of (2069) professor. The research based on hypothesis model which reflect the research hypotheses from main variables presented  the leadership virtuousness (optimism, forgiveness, trust, compassion and  integrity) for moderating affect with the workplace fun (fun activities, Coworker socializing, manager support for fun). The organizational brilliance will increase in case of providing sub-variables which (leadership brilliance, service & innovation brillianc

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Publication Date
Fri Jul 12 2013
Journal Name
Journal Of Biosciences
A functional connection of Dictyostelium paracaspase with the contractile vacuole and a possible partner of the vacuolar proton ATPase
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Publication Date
Fri Jan 01 2016
Journal Name
International Journal Of Surgery Case Reports
Myositis ossificans: A rare location in the foot. Report of a case and review of literature
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