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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 Dec 15 2021
Journal Name
Abstract And Applied Analysis
Dynamical Behaviors of a Fractional-Order Three Dimensional Prey-Predator Model
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In this paper, the dynamical behavior of a three-dimensional fractional-order prey-predator model is investigated with Holling type III functional response and constant rate harvesting. It is assumed that the middle predator species consumes only the prey species, and the top predator species consumes only the middle predator species. We also prove the boundedness, the non-negativity, the uniqueness, and the existence of the solutions of the proposed model. Then, all possible equilibria are determined, and the dynamical behaviors of the proposed model around the equilibrium points are investigated. Finally, numerical simulations results are presented to confirm the theoretical results and to give a better understanding of the dynami

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Publication Date
Fri May 18 2018
Journal Name
Thesis
The Arabian killifish (Aphanius dispar) as a novel model for mycophysiological studies.
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Abstract Candida albicans is a commensal fungal pathogen that grows in yeast and hyphal forms in the human gut. C. albicans causes mucosal and cutaneous diseases that can result in significant mortality following systematic infections and it also exhibits drug resistance. Zebrafish have been an excellent model to investigate C. albicans infections because of their transparency and the availability of many transgenic lines. However, there is a limitation in using zebrafish as a model because the fish embryos cannot survive at 37°C therefore it is not suitable for studying Candida infections at physiological relevant human body temperature. In this thesis, the normal embryonic development of Arabian killifish (A. dispar) is investigated, rev

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Publication Date
Thu Feb 01 2024
Journal Name
Russian Journal Of Bioorganic Chemistry
Synthesis, Identification, Antioxidant, Molecular Docking, and In Silico ADME Study for Some New Derivatives Containing Thiourea Moiety
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Objective: Synthesized a series of new thiourea (TU) derivatives, tested their antioxidant activity, and investigated their expected biological activity by theoretical study (computational methods). Methods: The derivatives were made using a one-pot reaction with two steps. Initially, succinyl chloride was mixed with KSCN to make succinyl isothiocyanate. Then, primary and secondary amines were used to make TU derivatives. The theoretical studies were done by Swiss ADME and molecular docking via Genetic Optimization of Linkage Docking (GOLD). Then evaluate antioxidant activity using the DPPH scavenging method. Results: FT-IR, 1H NMR, and 13C NMR spectroscopy show the verification of all the prepared derivatives. Compounds (II), (VIII),

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Publication Date
Sun Mar 12 2023
Journal Name
المجلة الدولية للتنمية في العلوم الاجتماعية والإنسانية
the Ottoman Empire in the Nineteenth Century (Iraq as a Model)the Ottoman Empire in the Nineteenth Century (Iraq as a Model)
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One of the most important features of American foreign activity during the second half of the 19th century was the encouragement of sending Protestant missionary missions to all countries around the world. The mission of these missions was facilitated by the weakened state of the Ottoman Empire, the increasing influence of European countries, and their interference in its internal affairs. Despite the Ottoman efforts to counter the activities of these missions, the American missionary missions adopted a well-planned strategy that suited the conditions of the region, aimed at achieving their goals through direct and indirect methods, including intervention in the field of education. These missions gave great importance to educational aspects

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Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Institutional Performance Assessment using a model of the European Foundation for Quality Management (EFQM) A case study at an organization
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The study aims to use the European Excellence Model (EFQM) in assessing the institutional performance of the National Center for Administrative Development and Information Technology in order to determine the gap between the actual reality of the performance of the Center and the standards adopted in the model, in order to know the extent to which the Center seeks to achieve excellence in performance to improve the level of services provided and the adoption of methods Modern and contemporary management in the evaluation of its institutional performance.

The problem of the study was the absence of an institutional performance evaluation system at the centre whereby weaknesses (areas of improvement) and st

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Publication Date
Thu Jun 06 2024
Journal Name
Bulletin Of The Iraqi Natural History Meseum
Morphological and molecular study of three species of Acrobeloides (Cobb, 1924) Thorn, 1937(Rhabdida, Cephalobidae) as new record in Iraq
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Publication Date
Wed Aug 28 2024
Journal Name
World Academy Of Sciences Journal
Serum angiopoietin‑1 as a biomarker of missed miscarriage
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
A Comparative Study of Various Intelligent Algorithms Based Nonlinear PID Neural Trajectory Tracking Controller for the Differential Wheeled Mobile Robot Model
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This paper presents a comparative study of two learning algorithms for the nonlinear PID neural trajectory tracking controller for mobile robot in order to follow a pre-defined path. As simple and fast tuning technique, genetic and particle swarm optimization algorithms are used to tune the nonlinear PID neural controller's parameters to find the best velocities control actions of the right wheel and left wheel for the real mobile robot. Polywog wavelet activation function is used in the structure of the nonlinear PID neural controller. Simulation results (Matlab) and experimental work (LabVIEW) show that the proposed nonlinear PID controller with PSO
learning algorithm is more effective and robust than genetic learning algorithm; thi

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Publication Date
Sun Dec 01 2024
Journal Name
مجلة كلية التربية للبنات/ الجامعة العراقية
HURIER Model as a Model in Language Teaching
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Between the 1980s and 1990s, the HURIER model was developed by Brownell and consist of six interrelated components, which are represented in these acronyms (Hearing, Understanding, Remembering, Interpreting, Evaluating, and Responding). This model can be considered as a framework of the behavioral approach which can be used to improve students’ listening performance and to foster a positive attitude toward listening. Many learners find it challenging to improve their listening skills when learning a second or foreign language because it requires the integration of both listening and speaking. Consequently, enhancing this skill will help students improve other language skills, including reading, speaking, and writing. The HURI

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Publication Date
Tue Jan 01 2013
Journal Name
Journal Of The College Of Languages (jcl)
A Study in Tess of the D’Urbervilles as A Call for Liberal Education for Women
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Amongst the literary writers who used their art to direct the attention towards the issue of woman and her rights in a proper life is the English poet and novelist Thomas Hardy (1840-1928), who has been praised for his “openness to the feminine principle” 1 as Irving Howe put it. Hardy’s wide readings have changed his way of dealing with and thinking about so many critical issues which started to float on the surface of the English society during the mid and late of the 19th century. His readings for a number of writers, who seem of huge impact on his writings as he later admits that – “[his] pages show harmony of view with

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