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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 Jan 01 2022
Journal Name
Proceeding Of The 1st International Conference On Advanced Research In Pure And Applied Science (icarpas2021): Third Annual Conference Of Al-muthanna University/college Of Science
A theoretical study including the breakdown voltage characteristics for some industrial gases
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Industrial characteristics calculations concentrated on the physical properties for break down voltage in sf6, cf4 gases and their mixture with different concentrations are presented in our work. Calculations are achieved by using an improved modern code simulated on windows technique. Our results give rise to a compatible agreement with the other experimental published data.

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Publication Date
Thu Oct 06 2022
Journal Name
Advances In Systems Science And Applications
Stability and Bifurcation of a Delay Cancer Model in the Polluted Environment
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It is well known that the spread of cancer or tumor growth increases in polluted environments. In this paper, the dynamic behavior of the cancer model in the polluted environment is studied taking into consideration the delay in clearance of the environment from their contamination. The set of differential equations that simulates this epidemic model is formulated. The existence, uniqueness, and the bound of the solution are discussed. The local and global stability conditions of disease-free and endemic equilibrium points are investigated. The occurrence of the Hopf bifurcation around the endemic equilibrium point is proved. The stability and direction of the periodic dynamics are studied. Finally, the paper is ended with a numerical simul

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Publication Date
Sun Jan 01 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
The dynamics of a delayed ecological model with predator refuge and cannibalism
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This study has contributed to understanding a delayed prey-predator system involving cannibalism. The system is assumed to use the Holling type II functional response to describe the consuming process and incorporates the predator’s refuge against the cannibalism process. The characteristics of the solution are discussed. All potential equilibrium points have been identified. All equilibrium points’ local stability analyses for all time delay values are investigated. The system exhibits a Hopf bifurcation at the coexistence equilibrium, which is further demonstrated. The center manifold and normal form theorems for functional differential equations are then used to establish the direction of Hopf bifurcation and the stability of the per

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Publication Date
Sun Dec 16 2018
Journal Name
Al-academy
Philosophy of Precognitive Dream in the American Film (Minority Report - a Model)
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When we talk about the foresight in films, it is necessary to talk about dreams because foresight represents one of its distinct types. The Precognitive vision has become a possible material in dealing with as subjects in the film industry that adopt these ideas with their philosophical and scientific orientations, because they represent the imagination that predictors are specialized with. It can be invested through the introduction of a vision of another kind to achieve its goals and ambitions in the film industry and in particular the huge institutions of production as in Hollywood. The cinema works in the light of those concepts of production which found the prognostic dream (the foresight) as a distinctive genre in its films,
Th

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Publication Date
Wed Nov 20 2024
Journal Name
Future Medicinal Chemistry
New 4-amino-3-chloro benzoate ester derivatives as EGFR inhibitors: synthesis, in silico and biological analyses
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Publication Date
Sat Jul 26 2025
Journal Name
Arab World English Journal
YouTube as a Learning Tool Among EFL Learners: A Systematic Review
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This review paper examines the crucial impact of YouTube on learning English as a Foreign Language. Recently, learners’ interaction and development of their skills have been improved due to the integration of digital platforms into language education. YouTube is regarded as one of the most prevalent platforms due to its accessibility, multimodal content, and capacity to simulate real-life communication. This study tackles thirty selected research articles from various cultural and institutional backgrounds to identify the pedagogical benefits and challenges associated with using YouTube in teaching English. Conventional methods of teaching English as a foreign language encounter difficulties in improving students’ engagement and

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Publication Date
Sun Jan 11 2026
Journal Name
Journal Mustansiriyah Of Sports Science
A comparative study of mental abilities and athletic achievement motivation among students of the College of Physical Education and Sports Sciences at the University of Baghdad
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Publication Date
Sat Oct 01 2011
Journal Name
Journal Of Engineering
MECHANICAL DEGRADATION OF HIGH MOLECULAR WEIGHT POLYMER WITH SURFACTANT ADDITION IN A ROTATING DISK APPARATUS
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Mechanical degradation hampers the practical usage of polymers for turbulent drag reduction
application. Mechanical degradation refers to the chemical process in which the activation energy of
polymer chain scission is exceeded by mechanical action on the polymer chain, and bond rupture
occurs. When a water-soluble polymer and surfactant are mixed in water solution, the specific structures
(aggregates) are formed, in which polymer film is formed around micelle. In this work, Xanthan gum (XG) –
Sodium lauryl ether sulfate (SELS) complex formation and its effect on percentage viscosity reduction
(%VR) was studied. It was found that SELS surfactant reduced the mechanical degradation of XG much
more efficiently than th

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Publication Date
Sun Sep 27 2020
Journal Name
Journal Of The College Of Education For Women
Imagination and Emotional Impact by Constructional Methods:Al-Almohdeen’s (Believers’) Poetry in AhlAl-Bayt, (peace be upon them) as a Model
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The language that consists of only twenty-eight letters, but it is so broad that we are unable to understand it from all sides and this expansion is mainly caused by imagination, so Arab imagination, whose language goes in all directions And as it always responds to our ears, ancient critics divide imagination into holistic and partial But the language is not limited to these parts only. Do we wonder, where is the structural method of wishing, hope, questions and other methods of all this? In this paper, we try to show the importance of the method of writing in moving imagination in an interactive way, and what is related to human feelings in most, if not all, of its methods By studying the poetry of the believers in the Ahl al-Bayt, pea

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Publication Date
Sat Dec 30 2023
Journal Name
Journal Of Economics And Administrative Sciences
Financial Variables and Their Effects on The Development of Bank Credit and Productive Sectors in Iraq Using a Path Analysis Model
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This study aims to measure and analyze the direct and indirect effects of the financial variables, namely (public spending, public revenues, internal debt, and external debt), on the non-oil productive sectors with and without bank credit as an intermediate variable, using quarterly data for the period (2004Q1–2021Q4), converted using Eviews 12. To measure the objective of the study, the path analysis method was used using IBM SPSS-AMOS. The study concluded that the direct and indirect effects of financial variables have a weak role in directing bank credit towards the productive sectors in Iraq, which amounted to (0.18), as a result of market risks or unstable expectations in the economy. In addition to the weak credit ratings of borr

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